| Field | Description |
|---|---|
| SampleID | Name of the sample |
| TrimReads | Total number of reads after quality filtering |
| MeanReadLen | Average read length after quality filtering |
| Contigs | Number of contigs of the draft genome (>200bp) |
| GenomeLength | Length (bp) of the draft genome |
| LargestContig | Length (bp) of the largest contig in the genome |
| N50 | Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly |
| GC-Content | GC content (%) of the draft genome |
| Depth | Number of times each nucleotide position in the draft genome has a read that aligns to that position |
| SampleID | TrimReads | MeanReadLen | Contigs | GenomeLength | LargestContig | N50 | GC-Content | Depth |
|---|---|---|---|---|---|---|---|---|
| ID003II | 440193 | 235 | 2738 | 11624023 | 93753 | 10830 | 55.68 | 8X |
| ID012II | 189432 | 229 | 74 | 4027781 | 364375 | 119014 | 39.01 | 10X |
| ID014II | 372138 | 222 | 538 | 9335120 | 199730 | 41879 | 44.26 | 8X |
| ID030 | 658388 | 226 | 1953 | 7910850 | 164063 | 11044 | 53.55 | 18X |
| ID063 | 404133 | 239 | 146 | 4729069 | 314511 | 101315 | 50.83 | 20X |
| ID089 | 342534 | 223 | 135 | 4796271 | 223487 | 90807 | 37.92 | 15X |
| ID186 | 336786 | 232 | 45 | 3883370 | 473175 | 202592 | 38.93 | 20X |
| ID259 | 461494 | 239 | 289 | 5033855 | 131448 | 38437 | 55.64 | 21X |
| ORTHO015E | 206893 | 219 | 81 | 3977132 | 340368 | 123633 | 39.09 | 11X |
| ORTHO037E | 407540 | 218 | 54 | 3886703 | 358132 | 155954 | 38.94 | 22X |
| ORTHO047E | 443635 | 240 | 364 | 5147002 | 147377 | 32206 | 55.08 | 20X |
| ORTHO05E | 1031 | 249 | 377 | 137839 | 2786 | 362 | 40.19 | 1X |
| ORTHO082EII | 150557 | 244 | 3692 | 9881394 | 65119 | 5466 | 61.88 | 3X |
Average number of reads per sample = 339596
Average read length per sample = 232 bp
Average number of contigs per sample = 807
Average genome length per sample = 5720801 bp
Average largest contig length per sample = 221410 bp
Average N50 per sample = 71811 bp
Average GC content per sample = 47%
Average sequencing depth = 13.615X
| Field | Description |
|---|---|
| GenomePosition | Position in the genome where SNP is found |
| Type | Nature of the SNP identified (Only ‘True’ SNPs are shown by default) |
| ReferenceAllele | Allele found in the reference genome |
| AlternateAllele | Allele found in the genome of interest forming the SNP |
| Consequence | Amino acid alterations caused by the SNP |
| AffectedGene | The tartget gene affected by the SNP |
| Product | The outcome from the presence of the SNP |
## Error in read.table("ID003II_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
## Error in as.data.frame(snps): object 'snps' not found
## Error in cbind(snps[, 1:7]): object 'snps' not found
## Error in colnames(snpsdata) = c("GenomePosition", "Type", "ReferenceAllele", : object 'snpsdata' not found
## Error in eval(expr, envir, enclos): object 'snpsdata' not found
## Error in row.names(snps) = NULL: object 'snps' not found
## Error in nrow(snps): object 'snps' not found
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ID014II_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ID030_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ID063_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ID089_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ID259_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | NA | copper resistance protein NlpE N-terminal domain-containing protein |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | NA | copper resistance protein NlpE N-terminal domain-containing protein |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | NA | copper resistance protein NlpE N-terminal domain-containing protein |
| 61728 | snp | T | C | missense_variant c.4274066A>G p.His1424689Arg | NA | copper resistance protein NlpE N-terminal domain-containing protein |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | NA | copper resistance protein NlpE N-terminal domain-containing protein |
| 61930 | snp | G | A | missense_variant c.4273864C>T p.Pro1424622Ser | NA | copper resistance protein NlpE N-terminal domain-containing protein |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | NA | quaternary ammonium compound resistance protein |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | NA | quaternary ammonium compound resistance protein |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | NA | quaternary ammonium compound resistance protein |
| 2147520 | snp | G | T | missense_variant c.2188274C>A p.Ala729425Glu | NA | quaternary ammonium compound resistance protein |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | NA | quaternary ammonium compound resistance protein |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | NA | quaternary ammonium compound resistance protein |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | NA | quaternary ammonium compound resistance protein |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | NA | quaternary ammonium compound resistance protein |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | NA | quaternary ammonium compound resistance protein |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | NA | quaternary ammonium compound resistance protein |
| 2147613 | snp | A | G | missense_variant c.2188181T>C p.Val729394Ala | NA | quaternary ammonium compound resistance protein |
| 3296382 | snp | C | T | missense_variant c.1039412G>A p.Arg346471Gln | NA | HdeD family acid-resistance protein |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | NA | HdeD family acid-resistance protein |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | NA | HdeD family acid-resistance protein |
| 3296631 | snp | T | A | missense_variant c.1039163A>T p.His346388Leu | NA | HdeD family acid-resistance protein |
| 3296659 | snp | C | T | missense_variant c.1039135G>A p.Val346379Ile | NA | HdeD family acid-resistance protein |
| 3296712 | snp | C | T | missense_variant c.1039082G>A p.Arg346361Gln | NA | HdeD family acid-resistance protein |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | NA | HdeD family acid-resistance protein |
| 3296799 | snp | A | C | missense_variant c.1038995T>G p.Phe346332Cys | NA | HdeD family acid-resistance protein |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | NA | HdeD family acid-resistance protein |
| 3296833 | snp | C | T | missense_variant c.1038961G>A p.Ala346321Thr | NA | HdeD family acid-resistance protein |
| 3468201 | snp | A | G | missense_variant c.867593T>C p.Leu289198Pro | NA | organic hydroperoxide resistance protein |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | NA | organic hydroperoxide resistance protein |
| 3468244 | snp | A | G | missense_variant c.867550T>C p.Tyr289184His | NA | organic hydroperoxide resistance protein |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | NA | organic hydroperoxide resistance protein |
| 3504715 | snp | C | T | missense_variant c.831079G>A p.Val277027Ile | NA | copper resistance system multicopper oxidase |
| 3504820 | snp | C | T | missense_variant c.830974G>A p.Gly276992Ser | NA | copper resistance system multicopper oxidase |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | NA | copper resistance system multicopper oxidase |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | NA | copper resistance system multicopper oxidase |
| 3505542 | snp | T | C | missense_variant c.830252A>G p.Lys276751Arg | NA | copper resistance system multicopper oxidase |
| 3505575 | snp | G | A | missense_variant c.830219C>T p.Thr276740Ile | NA | copper resistance system multicopper oxidase |
| 3505587 | snp | A | G | missense_variant c.830207T>C p.Val276736Ala | NA | copper resistance system multicopper oxidase |
| 3505642 | snp | G | A | missense_variant c.830152C>T p.Pro276718Ser | NA | copper resistance system multicopper oxidase |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | NA | copper resistance system multicopper oxidase |
| 3505861 | snp | C | T | missense_variant c.829933G>A p.Ala276645Thr | NA | copper resistance system multicopper oxidase |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | NA | copper resistance system multicopper oxidase |
| 3506433 | snp | T | A | missense_variant c.829361A>T p.Asp276454Val | NA | copper resistance system multicopper oxidase |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | NA | copper resistance protein B |
| 3506631 | snp | C | T | missense_variant c.829163G>A p.Gly276388Glu | NA | copper resistance protein B |
| 3506650 | snp | G | A | missense_variant c.829144C>T p.Leu276382Phe | NA | copper resistance protein B |
| 3506670 | snp | G | A | missense_variant c.829124C>T p.Pro276375Leu | NA | copper resistance protein B |
| 3506688 | snp | T | A | missense_variant c.829106A>T p.Gln276369Leu | NA | copper resistance protein B |
| 3506718 | snp | T | C | missense_variant c.829076A>G p.His276359Arg | NA | copper resistance protein B |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | NA | copper resistance protein B |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | NA | copper resistance protein B |
| 3506809 | snp | G | A | missense_variant c.828985C>T p.Pro276329Ser | NA | copper resistance protein B |
| 3506845 | snp | C | G | missense_variant c.828949G>C p.Ala276317Pro | NA | copper resistance protein B |
| 3506886 | snp | G | A | missense_variant c.828908C>T p.Ala276303Val | NA | copper resistance protein B |
| 3506895 | snp | C | T | missense_variant c.828899G>A p.Arg276300Lys | NA | copper resistance protein B |
| 3506950 | snp | T | C | missense_variant c.828844A>G p.Ser276282Gly | NA | copper resistance protein B |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | NA | copper resistance protein B |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | NA | copper resistance protein B |
| 3507176 | snp | G | A | missense_variant c.674G>A p.Gly225Glu | NA | copper resistance protein B |
| 3507182 | snp | G | A | missense_variant c.680G>A p.Gly227Asp | NA | copper resistance protein B |
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ORTHO047E_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ORTHO05E_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
## Error in read.table("ORTHO082EII_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
| GenomePosition | Type | ReferenceAllele | AlternateAllele | Consequence | AffectedGene | Product |
|---|---|---|---|---|---|---|
| 61633 | snp | T | A | missense_variant c.4274161A>T p.Ile1424721Phe | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61642 | snp | A | T | missense_variant c.4274152T>A p.Phe1424718Ile | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61695 | snp | C | T | missense_variant c.4274099G>A p.Ser1424700Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61761 | snp | A | G | missense_variant c.4274033T>C p.Ile1424678Thr | copper resistance protein NlpE N-terminal domain-containing protein | |
| 61898 | snp | G | A | missense_variant c.374G>A p.Ser125Asn | copper resistance protein NlpE N-terminal domain-containing protein | |
| 2147379 | snp | T | C | missense_variant c.2188415A>G p.Lys729472Arg | quaternary ammonium compound resistance protein | |
| 2147454 | snp | G | A | missense_variant c.2188340C>T p.Pro729447Leu | quaternary ammonium compound resistance protein | |
| 2147484 | snp | G | A | missense_variant c.2188310C>T p.Ala729437Val | quaternary ammonium compound resistance protein | |
| 2147496 | snp | A | G | missense_variant c.2188298T>C p.Phe729433Ser | quaternary ammonium compound resistance protein | |
| 2147520 | snp | G | C | missense_variant c.2188274C>G p.Ala729425Gly | quaternary ammonium compound resistance protein | |
| 2147529 | snp | T | A | missense_variant c.2188265A>T p.Gln729422Leu | quaternary ammonium compound resistance protein | |
| 2147538 | snp | G | A | missense_variant c.2188256C>T p.Ser729419Leu | quaternary ammonium compound resistance protein | |
| 2147544 | snp | G | T | missense_variant c.2188250C>A p.Ala729417Asp | quaternary ammonium compound resistance protein | |
| 2147559 | snp | A | T | missense_variant c.2188235T>A p.Leu729412Gln | quaternary ammonium compound resistance protein | |
| 2147568 | snp | T | G | missense_variant c.2188226A>C p.His729409Pro | quaternary ammonium compound resistance protein | |
| 2147574 | snp | G | A | missense_variant c.2188220C>T p.Ser729407Phe | quaternary ammonium compound resistance protein | |
| 3296460 | snp | C | T | missense_variant c.1039334G>A p.Arg346445His | HdeD family acid-resistance protein | |
| 3296469 | snp | G | A | missense_variant c.1039325C>T p.Ala346442Val | HdeD family acid-resistance protein | |
| 3296550 | snp | A | G | missense_variant c.1039244T>C p.Leu346415Pro | HdeD family acid-resistance protein | |
| 3296619 | snp | A | G | missense_variant c.1039175T>C p.Leu346392Ser | HdeD family acid-resistance protein | |
| 3296656 | snp | T | C | missense_variant c.1039138A>G p.Lys346380Glu | HdeD family acid-resistance protein | |
| 3296736 | snp | G | T | missense_variant c.1039058C>A p.Thr346353Lys | HdeD family acid-resistance protein | |
| 3296763 | snp | G | A | missense_variant c.1039031C>T p.Pro346344Leu | HdeD family acid-resistance protein | |
| 3296814 | snp | G | A | missense_variant c.1038980C>T p.Ala346327Val | HdeD family acid-resistance protein | |
| 3442765 | snp | T | G | missense_variant c.893029A>C p.Ile297677Leu | nreB | nickel resistance MFS transporter NreB |
| 3468029 | snp | C | T | missense_variant c.867765G>A p.Met289255Ile | organic hydroperoxide resistance protein | |
| 3468216 | snp | A | G | missense_variant c.867578T>C p.Val289193Ala | organic hydroperoxide resistance protein | |
| 3468231 | snp | T | C | missense_variant c.867563A>G p.Tyr289188Cys | organic hydroperoxide resistance protein | |
| 3468300 | snp | G | A | missense_variant c.867494C>T p.Pro289165Leu | organic hydroperoxide resistance protein | |
| 3504660 | snp | C | A | missense_variant c.831134G>T p.Cys277045Phe | copper resistance system multicopper oxidase | |
| 3504723 | snp | C | T | missense_variant c.831071G>A p.Ser277024Asn | copper resistance system multicopper oxidase | |
| 3505158 | snp | A | G | missense_variant c.830636T>C p.Val276879Ala | copper resistance system multicopper oxidase | |
| 3505287 | snp | G | A | missense_variant c.830507C>T p.Ala276836Val | copper resistance system multicopper oxidase | |
| 3505723 | snp | G | C | missense_variant c.830071C>G p.Leu276691Val | copper resistance system multicopper oxidase | |
| 3505778 | snp | A | G | missense_variant c.1224A>G p.Ile408Met | copper resistance system multicopper oxidase | |
| 3505887 | snp | T | G | missense_variant c.829907A>C p.Glu276636Ala | copper resistance system multicopper oxidase | |
| 3505935 | snp | C | T | missense_variant c.829859G>A p.Gly276620Asp | copper resistance system multicopper oxidase | |
| 3506327 | snp | C | G | missense_variant c.829467G>C p.Lys276489Asn | copper resistance system multicopper oxidase | |
| 3506624 | snp | C | G | missense_variant c.829170G>C p.Arg276390Ser | copper resistance protein B | |
| 3506688 | snp | T | G | missense_variant c.829106A>C p.Gln276369Pro | copper resistance protein B | |
| 3506736 | snp | G | A | missense_variant c.829058C>T p.Pro276353Leu | copper resistance protein B | |
| 3506761 | snp | G | T | missense_variant c.829033C>A p.Leu276345Met | copper resistance protein B | |
| 3506781 | snp | A | G | missense_variant c.829013T>C p.Leu276338Pro | copper resistance protein B | |
| 3506932 | snp | C | A | missense_variant c.828862G>T p.Asp276288Tyr | copper resistance protein B | |
| 3506963 | snp | A | G | missense_variant c.461A>G p.Lys154Arg | copper resistance protein B | |
| 3506979 | snp | T | A | missense_variant c.828815A>T p.Glu276272Val | copper resistance protein B | |
| 3506995 | snp | C | A | missense_variant c.828799G>T p.Asp276267Tyr | copper resistance protein B | |
| 3507025 | snp | C | A | missense_variant c.828769G>T p.Val276257Leu | copper resistance protein B | |
| 3507039 | snp | C | G | missense_variant c.828755G>C p.Ser276252Thr | copper resistance protein B |
| Field | Description |
|---|---|
| Contig | Contig name where the gene was found |
| Start | Start position of the gene within the contig |
| End | End position of the gene within the contig |
| Gene | Antibiotic resistance gene |
| Gaps | Gaps in subject (genome) and query (antibiotic resistance gene) |
| Coverage | Proportion (%) of the gene covered |
| Identity | Proportion (%) of exact nucleotide matches |
| Accession | Accesion number of the antibiotic resistance gene |
| Product | Antibiotic resistance gene product |
| Resistance | Antibiotic that the gene confers resistance to |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig01177 | 71 | 931 | aac(3)-IId_1 | 0/0 | 100.0 | 99.9 | EU022314 | aac(3)-IId | Gentamicin, Tobramycin |
| contig00154 | 13860 | 14662 | aadA2_1 | 0/0 | 98.0 | 99.9 | NC_010870 | aadA2 | Streptomycin |
| contig00463 | 4721 | 5254 | ant(2’’)-Ia_13 | 0/0 | 100.0 | 99.1 | DQ176450 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00988 | 2040 | 2573 | ant(2’’)-Ia_13 | 0/0 | 100.0 | 99.8 | DQ176450 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00474 | 3794 | 4597 | aph(3’’)-Ib_5 | 0/0 | 100.0 | 100.0 | AF321551 | aph(3’’)-Ib | Streptomycin |
| contig01476 | 48 | 863 | aph(3’)-Ia_7 | 0/0 | 100.0 | 100.0 | X62115 | aph(3’)-Ia | |
| contig02215 | 25 | 783 | aph(3’)-VIa_1 | 0/0 | 97.3 | 100.0 | X07753 | aph(3’)-VIa | Amikacin |
| contig00474 | 2958 | 3794 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00988 | 1056 | 1922 | blaCARB-2_1 | 0/0 | 100.0 | 100.0 | M69058 | blaCARB-2 | Ampicillin, Amoxicillin, Piperacillin |
| contig00966 | 1160 | 1972 | blaNDM-1_1 | 0/0 | 100.0 | 100.0 | FN396876 | blaNDM-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam |
| contig00812 | 1447 | 2277 | blaOXA-1_1 | 0/0 | 100.0 | 100.0 | HQ170510 | blaOXA-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig01290 | 1049 | 1838 | blaOXA-22_1 | 0/0 | 95.8 | 99.9 | AF064820 | blaOXA-22 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig00197 | 9252 | 10094 | blaOXA-420_1 | 0/0 | 100.0 | 100.0 | AB983359 | blaOXA-420 | |
| contig01773 | 33 | 848 | blaOXA-60_1 | 0/0 | 100.0 | 100.0 | AF525303 | blaOXA-60 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Imipenem |
| contig00812 | 696 | 1328 | catB3_2 | 0/0 | 100.0 | 99.8 | U13880 | catB3 | Chloramphenicol |
| contig00192 | 1187 | 2452 | cmlB1_1 | 0/0 | 100.0 | 99.8 | AM296481 | cmlB1 | Chloramphenicol |
| contig01358 | 1213 | 1686 | dfrA5_1 | 0/0 | 100.0 | 100.0 | X12868 | dfrA5 | Trimethoprim |
| contig00785 | 1240 | 2453 | floR_2 | 0/0 | 99.9 | 98.3 | AF118107 | floR | Chloramphenicol, Florfenicol |
| contig01609 | 131 | 1052 | mph(A)_2 | 1/1 | 100.0 | 99.6 | U36578 | mph(A) | Erythromycin, Azithromycin, Spiramycin, Telithromycin |
| contig00891 | 111 | 995 | mph(E)_1 | 0/0 | 100.0 | 100.0 | DQ839391 | mph(E) | Erythromycin |
| contig00891 | 1051 | 2526 | msr(E)_1 | 0/0 | 100.0 | 100.0 | FR751518 | msr(E) | |
| contig01714 | 93 | 959 | sul1_5 | 0/0 | 100.0 | 99.9 | EU780013 | sul1 | Sulfamethoxazole |
| contig01812 | 316 | 1128 | sul2_2 | 0/0 | 99.6 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00971 | 143 | 1375 | tet(31)_1 | 0/0 | 100.0 | 100.0 | GQ283908 | tet(31) | Doxycycline, Tetracycline |
| contig00474 | 867 | 2042 | tet(G)_2 | 0/0 | 100.0 | 100.0 | AF133140 | tet(G) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig01177 | 71 | 931 | AAC(3)-IId | 0/0 | 100.0 | 99.9 | EU022314.1:0-861 | AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli | aminoglycoside |
| contig00154 | 13860 | 14639 | aadA2 | 0/0 | 100.0 | 100.0 | AF156486:5012-5792 | aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp. | aminoglycoside |
| contig00463 | 4721 | 5254 | ANT(2’’)-Ia | 0/0 | 100.0 | 98.9 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig00988 | 2040 | 2573 | ANT(2’’)-Ia | 0/0 | 100.0 | 99.2 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig00474 | 3794 | 4597 | APH(3’’)-Ib | 0/0 | 100.0 | 99.8 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig01476 | 48 | 863 | APH(3’)-Ia | 0/0 | 100.0 | 100.0 | BX664015.1:103833-103017 | APH(3’)-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3’)-Ic an aminoglycoside phosphotransferase encoded by plasmids transposons and genomic islands in K. pneumoniae A. baumannii S. marcescens Corynebacterium spp. Photobacterium spp. and Citrobacter spp. | aminoglycoside |
| contig02215 | 25 | 783 | APH(3’)-VIa | 0/0 | 97.3 | 100.0 | X07753:102-882 | APH(3’)-VIa is a plasmid-encoded aminoglycoside phosphotransferase in A. baumannii | aminoglycoside |
| contig00474 | 2958 | 3794 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00988 | 1056 | 1970 | CARB-3 | 0/0 | 100.0 | 99.9 | S46063:121-1036 | CARB-3 is a beta-lactamase found in Pseudomonas aeruginosa | penam |
| contig00812 | 696 | 1328 | catB3 | 0/0 | 100.0 | 99.8 | JX101693.1:58200-58833 | catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli | phenicol |
| contig00192 | 1187 | 2452 | cmlB1 | 0/0 | 100.0 | 99.8 | AM296481:775-2041 | cmlB1 is a plasmid-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica | phenicol |
| contig00966 | 1976 | 2341 | determinant_of_bleomycin_resistance | 0/0 | 100.0 | 100.0 | KC503911.1:9883-10249 | A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. | glycopeptide |
| contig01358 | 1213 | 1686 | dfrA5 | 0/0 | 100.0 | 100.0 | DQ278190:0-474 | dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae | diaminopyrimidine |
| contig00785 | 1239 | 2453 | floR | 0/0 | 100.0 | 99.9 | AF231986:3307-4522 | floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae | phenicol |
| contig01609 | 147 | 1052 | mphA | 0/0 | 100.0 | 99.9 | D16251.1:2531-1625 | The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner. | macrolide |
| contig00891 | 111 | 995 | mphE | 0/0 | 100.0 | 100.0 | DQ839391.1:13757-12872 | mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 | macrolide |
| contig00891 | 1051 | 2526 | msrE | 0/0 | 100.0 | 100.0 | EU294228.1:21241-22717 | MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. | lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline |
| contig00966 | 1160 | 1972 | NDM-1 | 0/0 | 100.0 | 100.0 | FN396876:3219-2406 | NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. | carbapenem, cephalosporin, cephamycin, penam |
| contig00812 | 1447 | 2277 | OXA-1 | 0/0 | 100.0 | 100.0 | JN420336.1:2230-1399 | OXA-1 is a beta-lactamase found in E. coli | cephalosporin, penam |
| contig01290 | 1049 | 1838 | OXA-22 | 0/0 | 95.8 | 99.9 | AF064820:951-1776 | OXA-22 is a beta-lactamase found in Ralstonia pickettii | cephalosporin, penam |
| contig00197 | 9252 | 10094 | OXA-420 | 0/0 | 100.0 | 100.0 | AB983359:2425-3268 | From the Lahey list of beta-lactamases. Not yet released. | cephalosporin, penam |
| contig01773 | 33 | 848 | OXA-60 | 0/0 | 100.0 | 100.0 | AF525303:2770-3586 | OXA-60 is a beta-lactamase found in Ralstonia pickettii | cephalosporin, penam |
| contig01358 | 691 | 1023 | qacH | 0/0 | 100.0 | 99.4 | DQ149925.1:188-521 | qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae | fluoroquinolone |
| contig01714 | 93 | 932 | sul1 | 0/0 | 100.0 | 100.0 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig01812 | 316 | 1128 | sul2 | 0/0 | 99.6 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00971 | 143 | 1375 | tet(31) | 0/0 | 100.0 | 99.8 | AJ250203:1650-2883 | Tet31 is a tetracycline efflux pump found in Aeromonas salmonicida a Gram-negative bacteria. It has also been shown to be expressed in Gallibacterium anatis. | tetracycline |
| contig00474 | 867 | 2042 | tet(G) | 0/0 | 100.0 | 92.8 | AF133139:0-1176 | TetG is a tetracycline efflux protein found in Gram-negative bacteria. The encoding gene is found in both chromosomal and plasmid DNA where it is frequently linked to the floR sul1 and cmlA9 genes which encode proteins that can confer florfenicol/chloramphenicol sulfamethoxazole and chloramphenicol resistance respectively. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig01177 | 71 | 931 | (AGly)aac3-IId | 0/0 | 100.0 | 99.9 | EU022314:1-861 | (AGly)aac3-IId | NA |
| contig00812 | 2377 | 3181 | (AGly)aadA1-pm | 0/0 | 96.9 | 99.8 | JQ690540:7968-8798 | (AGly)aadA1-pm | NA |
| contig00154 | 13860 | 14639 | (AGly)aadA2 | 0/0 | 100.0 | 100.0 | X68227:66-945 | (AGly)aadA2 | NA |
| contig00463 | 4721 | 5254 | (AGly)aadB | 0/0 | 100.0 | 98.9 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig00988 | 2040 | 2573 | (AGly)aadB | 0/0 | 100.0 | 99.2 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig01476 | 48 | 863 | (AGly)aph(3’’)-Ia | 0/0 | 100.0 | 100.0 | FJ172370:38668-39483 | (AGly)aph(3’’)-Ia | NA |
| contig02215 | 25 | 783 | (AGly)aphA6 | 0/0 | 97.3 | 99.9 | JF949760:695-1474 | (AGly)aphA6 | NA |
| contig00474 | 3794 | 4597 | (AGly)strA | 0/0 | 100.0 | 99.9 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00474 | 2958 | 3794 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00966 | 1160 | 1972 | (Bla)blaNDM-1 | 0/0 | 100.0 | 100.0 | JQ080305:1-813 | (Bla)blaNDM-1 | NA |
| contig00812 | 1447 | 2277 | (Bla)blaOXA-1 | 0/0 | 100.0 | 100.0 | JQ682867:1-831 | (Bla)blaOXA-1 | NA |
| contig01290 | 1049 | 1838 | (Bla)blaOXA-22 | 0/0 | 95.8 | 99.9 | AF064820:952-1776 | (Bla)blaOXA-22 | NA |
| contig00197 | 9252 | 10094 | (Bla)blaOXA-58 | 0/0 | 100.0 | 99.6 | AY665723:3301-4143 | (Bla)blaOXA-58 | NA |
| contig01773 | 33 | 848 | (Bla)blaOXA-60 | 0/0 | 100.0 | 93.1 | AY664505:1-816 | (Bla)blaOXA-60 | NA |
| contig00988 | 1056 | 1970 | (Bla)CARB-3 | 0/0 | 100.0 | 99.9 | S46063:122-1036 | (Bla)CARB-3 | NA |
| contig01609 | 147 | 1052 | (MLS)mph(A) | 0/0 | 100.0 | 99.9 | DQ445270:1626-2531 | (MLS)mph(A) | NA |
| contig00891 | 111 | 995 | (MLS)mph(E) | 0/0 | 100.0 | 99.9 | JF769133:8777-9661 | (MLS)mph(E) | NA |
| contig00891 | 1051 | 2526 | (MLS)msr(E) | 0/0 | 100.0 | 100.0 | JF769133:7246-8721 | (MLS)msr(E) | NA |
| contig00812 | 696 | 1328 | (Phe)catB3 | 0/0 | 100.0 | 99.7 | AJ009818:883-1515 | (Phe)catB3 | NA |
| contig00192 | 1187 | 2452 | (Phe)cmlB1 | 0/0 | 100.0 | 99.8 | NG_036292:776-2041 | (Phe)cmlB1 | NA |
| contig00785 | 1239 | 2453 | (Phe)floR | 0/0 | 100.0 | 99.8 | AKLJ01000508:383-1597 | (Phe)floR | NA |
| contig01714 | 93 | 932 | (Sul)sul1 | 0/0 | 100.0 | 100.0 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig01812 | 316 | 1128 | (Sul)sul2 | 0/0 | 99.6 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00971 | 143 | 1375 | (Tet)tet(31) | 0/0 | 100.0 | 99.8 | AJ250203:1651-2883 | (Tet)tet(31) | NA |
| contig00474 | 867 | 2042 | (Tet)tetG | 0/0 | 100.0 | 100.0 | AF133140:757-1932 | (Tet)tetG | NA |
| contig00474 | 2146 | 2754 | (Tet)tetR(G) | 0/0 | 96.2 | 98.5 | S52438:113-745 | (Tet)tetR(G) | NA |
| contig01358 | 1213 | 1686 | (Tmt)dfrA5 | 0/0 | 100.0 | 100.0 | X12868:1306-1779 | (Tmt)dfrA5 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig01177 | 71 | 931 | aac(3)-IId | 0/0 | 100.0 | 100.0 | NG_047251.1 | aminoglycoside N-acetyltransferase AAC(3)-IId | GENTAMICIN |
| contig01358 | 48 | 602 | aac(6’)-Ib-G | 0/0 | 100.0 | 99.8 | NG_051697.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | GENTAMICIN |
| contig00812 | 2390 | 3181 | aadA1 | 0/0 | 100.0 | 99.9 | NG_052266.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 | STREPTOMYCIN |
| contig00154 | 13860 | 14651 | aadA2 | 0/0 | 100.0 | 100.0 | NG_051846.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2 | STREPTOMYCIN |
| contig00463 | 4721 | 5254 | ant(2’’)-Ia | 0/0 | 100.0 | 99.1 | NG_052432.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig00988 | 2040 | 2573 | ant(2’’)-Ia | 0/0 | 100.0 | 99.8 | NG_047389.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig00474 | 3794 | 4621 | aph(3’’)-Ib | 0/0 | 100.0 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig01476 | 48 | 863 | aph(3’)-Ia | 0/0 | 100.0 | 100.0 | NG_047431.1 | aminoglycoside O-phosphotransferase APH(3’)-Ia | KANAMYCIN |
| contig02215 | 25 | 783 | aph(3’)-VIa | 0/0 | 97.3 | 100.0 | NG_047448.1 | aminoglycoside O-phosphotransferase APH(3’)-VIa | AMIKACIN, KANAMYCIN |
| contig00474 | 2958 | 3794 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00988 | 1056 | 1922 | blaCARB-2 | 0/0 | 100.0 | 100.0 | NG_048722.1 | PSE family carbenicillin-hydrolyzing class A beta-lactamase CARB-2 | BETA-LACTAM |
| contig00966 | 1160 | 1972 | blaNDM-1 | 0/0 | 100.0 | 100.0 | NG_049326.1 | subclass B1 metallo-beta-lactamase NDM-1 | CARBAPENEM |
| contig00812 | 1447 | 2277 | blaOXA-1 | 0/0 | 100.0 | 100.0 | NG_049392.1 | oxacillin-hydrolyzing class D beta-lactamase OXA-1 | CEPHALOSPORIN |
| contig01290 | 1049 | 1838 | blaOXA-22 | 0/0 | 95.8 | 99.9 | NG_049518.1 | benzylpenicillin-hydrolyzing class D beta-lactamase OXA-22 | BETA-LACTAM |
| contig00197 | 9252 | 10094 | blaOXA-420 | 0/0 | 100.0 | 100.0 | NG_049708.1 | OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 | CARBAPENEM |
| contig01773 | 33 | 848 | blaOXA-60 | 0/0 | 100.0 | 100.0 | NG_049800.1 | carbapenem-hydrolyzing class D beta-lactamase OXA-60 | CARBAPENEM |
| contig00966 | 1976 | 2341 | ble-MBL | 0/0 | 100.0 | 100.0 | NG_047559.1 | bleomycin binding protein Ble-MBL | BLEOMYCIN |
| contig00812 | 696 | 1328 | catB3 | 0/0 | 100.0 | 99.8 | NG_047604.1 | type B-3 chloramphenicol O-acetyltransferase CatB3 | CHLORAMPHENICOL |
| contig00192 | 1187 | 2452 | cmlB1 | 0/0 | 100.0 | 99.8 | NG_047658.1 | chloramphenicol efflux MFS transporter CmlB1 | CHLORAMPHENICOL |
| contig01358 | 1213 | 1686 | dfrA5 | 0/0 | 100.0 | 100.0 | NG_051699.1 | trimethoprim-resistant dihydrofolate reductase DfrA5 | TRIMETHOPRIM |
| contig00785 | 1239 | 2453 | floR | 0/0 | 100.0 | 100.0 | NG_047869.1 | chloramphenicol/florfenicol efflux MFS transporter FloR | CHLORAMPHENICOL, FLORFENICOL |
| contig01609 | 131 | 1052 | mph(A) | 1/1 | 100.0 | 99.6 | NG_047986.1 | Mph(A) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00891 | 111 | 995 | mph(E) | 0/0 | 100.0 | 100.0 | NG_064660.1 | Mph(E) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00891 | 1051 | 2526 | msr(E) | 0/0 | 100.0 | 100.0 | NG_048007.1 | ABC-F type ribosomal protection protein Msr(E) | MACROLIDE |
| contig01714 | 93 | 932 | sul1 | 0/0 | 100.0 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| contig01812 | 316 | 1128 | sul2 | 0/0 | 99.6 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00971 | 143 | 1354 | tet(31) | 0/0 | 100.0 | 99.9 | NG_048123.1 | tetracycline efflux MFS transporter Tet(31) | TETRACYCLINE |
| contig00474 | 867 | 2042 | tet(G) | 0/0 | 100.0 | 100.0 | NG_051907.1 | tetracycline efflux MFS transporter Tet(G) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig01177 | 71 | 931 | AAC3 | 0/0 | 100.0 | 100.0 | MEG_64 | Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 | NA |
| contig00154 | 13860 | 14662 | ANT3-DPRIME | 0/0 | 98.0 | 99.9 | MEG_975 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00812 | 2377 | 3181 | ANT3-DPRIME | 0/0 | 96.9 | 99.8 | MEG_915 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00474 | 3794 | 4621 | APH3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig01476 | 48 | 863 | APH3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_1044 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig02215 | 25 | 783 | APH3-PRIME | 0/0 | 97.3 | 100.0 | MEG_1075 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-PRIME | NA |
| contig00474 | 2958 | 3794 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00966 | 1976 | 2341 | BRP | 0/0 | 100.0 | 100.0 | MEG_1477 | Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP | NA |
| contig00192 | 1187 | 2452 | CMLB | 0/0 | 100.0 | 99.8 | MEG_1775 | Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:CMLB | NA |
| contig01358 | 1213 | 1686 | DFRA | 0/0 | 100.0 | 100.0 | MEG_2546 | Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA | NA |
| contig00785 | 1239 | 2453 | FLOR | 0/0 | 100.0 | 100.0 | MEG_2923 | Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR | NA |
| contig01609 | 131 | 1052 | MPHA | 1/1 | 100.0 | 99.6 | MEG_4030 | Drugs:MLS:Macrolide_phosphotransferases:MPHA | NA |
| contig00891 | 111 | 995 | MPHE | 0/0 | 100.0 | 100.0 | MEG_4044 | Drugs:MLS:Macrolide_phosphotransferases:MPHE | NA |
| contig00891 | 1051 | 2526 | MSRE | 0/0 | 100.0 | 100.0 | MEG_4075 | Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE | NA |
| contig00966 | 1160 | 1972 | NDM | 0/0 | 100.0 | 100.0 | MEG_4143 | Drugs:betalactams:Class_B_betalactamases:NDM | NA |
| contig00197 | 9225 | 10100 | OXA | 0/0 | 96.2 | 99.5 | MEG_5259 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00812 | 1447 | 2277 | OXA | 0/0 | 100.0 | 100.0 | MEG_4980 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig01290 | 1049 | 1838 | OXA | 0/0 | 95.8 | 99.9 | MEG_4766 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig01773 | 33 | 848 | OXA | 0/0 | 100.0 | 100.0 | MEG_4779 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig01358 | 691 | 1023 | QACF | 0/0 | 100.0 | 100.0 | MEG_5838 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACF | NA |
| contig01714 | 1 | 933 | SULI | 0/0 | 96.4 | 100.0 | MEG_6615 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI | NA |
| contig01812 | 316 | 1128 | SULII | 0/0 | 99.6 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00971 | 143 | 1375 | TET31 | 0/0 | 100.0 | 100.0 | MEG_6968 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET31 | NA |
| contig00474 | 867 | 2042 | TETG | 0/0 | 100.0 | 100.0 | MEG_7077 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETG | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00060 | 1238 | 1771 | ant(2’’)-Ia_1 | 0/0 | 100.0 | 100.0 | X04555 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00052 | 3387 | 4189 | aph(3’’)-Ib_2 | 0/0 | 99.9 | 100.0 | AF024602 | aph(3’’)-Ib | Streptomycin |
| contig00060 | 372 | 1187 | aph(3’)-Ia_7 | 0/0 | 100.0 | 100.0 | X62115 | aph(3’)-Ia | |
| contig00052 | 2551 | 3387 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00001 | 9 | 1160 | blaADC-25_1 | 0/0 | 100.0 | 99.9 | EF016355 | blaADC-25 | |
| contig00027 | 47 | 889 | blaOXA-420_1 | 0/0 | 100.0 | 100.0 | AB983359 | blaOXA-420 | |
| contig00011 | 112601 | 113425 | blaOXA-69_1 | 0/0 | 100.0 | 100.0 | AY859527 | blaOXA-69 | Amoxicillin, Ampicillin |
| contig00040 | 21860 | 22369 | dfrA20_1 | 0/0 | 100.0 | 100.0 | AJ605332 | dfrA20 | Trimethoprim |
| contig00027 | 5534 | 6418 | mph(E)_1 | 0/0 | 100.0 | 100.0 | DQ839391 | mph(E) | Erythromycin |
| contig00027 | 6474 | 7949 | msr(E)_1 | 0/0 | 100.0 | 100.0 | FR751518 | msr(E) | |
| contig00063 | 277 | 1089 | sul2_2 | 0/0 | 99.6 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00027 | 11178 | 12299 | tet(39)_1 | 0/0 | 100.0 | 100.0 | KT346360 | tet(39) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00006 | 14076 | 15422 | abeM | 0/0 | 100.0 | 98.9 | AB204810:186-1533 | AbeM is an multidrug efflux pump found in Acinetobacter baumannii. | acridine_dye, fluoroquinolone, triclosan |
| contig00009 | 77409 | 77738 | abeS | 0/0 | 100.0 | 100.0 | CP001172.1:1249348-1249018 | AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. | aminocoumarin, macrolide |
| contig00029 | 28006 | 29295 | Acinetobacter_baumannii_AbaF | 0/0 | 100.0 | 97.9 | CP000521.1:1558523-1557233 | Expression of abaF in E. coli resulted in increased resistance to fosfomycin. | fosfomycin |
| contig00012 | 20581 | 21885 | Acinetobacter_baumannii_AbaQ | 0/0 | 100.0 | 100.0 | CP001182.2:2256889-2255584 | AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii | fluoroquinolone |
| contig00008 | 19900 | 21378 | Acinetobacter_baumannii_AmvA | 0/0 | 100.0 | 100.0 | FJ911554.1:176-1655 | AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. | acridine_dye, macrolide |
| contig00001 | 9 | 1160 | ADC-30 | 0/0 | 100.0 | 100.0 | JF265068.1:954-2106 | An ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii | cephalosporin |
| contig00031 | 12186 | 13376 | adeA | 0/0 | 100.0 | 97.7 | AF370885.1:3438-4629 | AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. | glycylcycline, tetracycline |
| contig00031 | 9079 | 12186 | adeB | 0/0 | 100.0 | 97.8 | AF370885.1:4628-7736 | AdeB is the multidrug transporter of the adeABC efflux system. | glycylcycline, tetracycline |
| contig00031 | 7605 | 9002 | adeC | 0/0 | 100.0 | 95.4 | CP013924.1:2063742-2065140 | AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels and is not essential for antibiotic resistance. | glycylcycline, tetracycline |
| contig00009 | 68465 | 71644 | adeF | 0/0 | 100.0 | 100.0 | CT025801.2:0-3180 | AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. | fluoroquinolone, tetracycline |
| contig00009 | 71651 | 72871 | adeG | 0/0 | 100.0 | 100.0 | CT025800.2:0-1221 | AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00009 | 67004 | 68455 | adeH | 0/0 | 100.0 | 100.0 | CT025802.2:0-1452 | AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00017 | 41693 | 42943 | adeI | 0/0 | 100.0 | 100.0 | CP001182.2:3283426-3284677 | AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00017 | 42956 | 46132 | adeJ | 0/0 | 100.0 | 99.6 | AY769962:2434-5611 | AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00017 | 46132 | 47586 | adeK | 0/0 | 100.0 | 98.7 | AY769962:5610-7065 | AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00009 | 73087 | 74100 | adeL | 0/0 | 100.0 | 99.4 | KR297239.1:1428-414 | AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. | fluoroquinolone, tetracycline |
| contig00008 | 75439 | 76092 | adeN | 0/0 | 100.0 | 98.0 | KF147862:0-654 | AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00031 | 13522 | 14265 | adeR | 0/0 | 100.0 | 100.0 | HM440348:0-744 | AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. | glycylcycline, tetracycline |
| contig00031 | 14297 | 15382 | adeS | 0/0 | 100.0 | 99.7 | HM440348:775-1861 | AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. | glycylcycline, tetracycline |
| contig00060 | 1238 | 1771 | ANT(2’’)-Ia | 0/0 | 100.0 | 100.0 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig00052 | 3387 | 4190 | APH(3’’)-Ib | 0/0 | 100.0 | 99.9 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00060 | 372 | 1187 | APH(3’)-Ia | 0/0 | 100.0 | 100.0 | BX664015.1:103833-103017 | APH(3’)-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3’)-Ic an aminoglycoside phosphotransferase encoded by plasmids transposons and genomic islands in K. pneumoniae A. baumannii S. marcescens Corynebacterium spp. Photobacterium spp. and Citrobacter spp. | aminoglycoside |
| contig00052 | 2551 | 3387 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00040 | 21860 | 22369 | dfrA20 | 0/0 | 100.0 | 100.0 | AJ605332:1303-1813 | dfrA20 is a plasmid-encoded dihydrofolate reductase found in Pasteurella multocida | diaminopyrimidine |
| contig00027 | 5534 | 6418 | mphE | 0/0 | 100.0 | 100.0 | DQ839391.1:13757-12872 | mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 | macrolide |
| contig00027 | 6474 | 7949 | msrE | 0/0 | 100.0 | 100.0 | EU294228.1:21241-22717 | MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. | lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline |
| contig00027 | 47 | 889 | OXA-420 | 0/0 | 100.0 | 100.0 | AB983359:2425-3268 | From the Lahey list of beta-lactamases. Not yet released. | cephalosporin, penam |
| contig00011 | 112601 | 113425 | OXA-69 | 0/0 | 100.0 | 100.0 | CU459141.1:2175316-2176141 | OXA-69 is a beta-lactamase found in A. baumannii | cephalosporin, penam |
| contig00063 | 277 | 1089 | sul2 | 0/0 | 99.6 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00027 | 11112 | 12299 | tet(39) | 0/0 | 100.0 | 100.0 | AY743590:0-1188 | Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00060 | 1238 | 1771 | (AGly)aadB | 0/0 | 100.0 | 100.0 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig00025 | 23905 | 24693 | (AGly)ant(3’’)-IIa | 0/0 | 100.0 | 98.9 | NG_054648:101-889 | (AGly)ant(3’’)-IIa | NA |
| contig00060 | 372 | 1187 | (AGly)aph(3’’)-Ia | 0/0 | 100.0 | 100.0 | FJ172370:38668-39483 | (AGly)aph(3’’)-Ia | NA |
| contig00052 | 3387 | 4190 | (AGly)strA | 0/0 | 100.0 | 100.0 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00052 | 2551 | 3387 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00012 | 7956 | 8975 | (Bla)BlaA1 | 0/0 | 100.0 | 99.9 | NC_010410:1803480-1804499 | (Bla)BlaA1 | NA |
| contig00022 | 41824 | 43098 | (Bla)BlaA2 | 0/0 | 100.0 | 100.0 | NC_010410:2507740-2509014 | (Bla)BlaA2 | NA |
| contig00001 | 9 | 1160 | (Bla)blaADC-30 | 0/0 | 100.0 | 100.0 | JF265068:955-2106 | (Bla)blaADC-30 | NA |
| contig00027 | 47 | 889 | (Bla)blaOXA-58 | 0/0 | 100.0 | 99.6 | AY665723:3301-4143 | (Bla)blaOXA-58 | NA |
| contig00011 | 112601 | 113425 | (Bla)blaOXA-69 | 0/0 | 100.0 | 100.0 | AY750911:1-825 | (Bla)blaOXA-69 | NA |
| contig00007 | 31147 | 31842 | (Bla)Mbl | 0/0 | 100.0 | 100.0 | NC_010410:c1997136-1996441 | (Bla)Mbl | NA |
| contig00001 | 314995 | 315957 | (Bla)Zn-dependent_hydrolase | 0/0 | 100.0 | 100.0 | NC_010410:882015-882977 | (Bla)Zn-dependent_hydrolase | NA |
| contig00027 | 5534 | 6418 | (MLS)mph(E) | 0/0 | 100.0 | 99.9 | JF769133:8777-9661 | (MLS)mph(E) | NA |
| contig00027 | 6474 | 7949 | (MLS)msr(E) | 0/0 | 100.0 | 100.0 | JF769133:7246-8721 | (MLS)msr(E) | NA |
| contig00063 | 277 | 1089 | (Sul)sul2 | 0/0 | 99.6 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00027 | 11112 | 12299 | (Tet)tet(39) | 0/0 | 100.0 | 100.0 | AY743590:749-1936 | (Tet)tet(39) | NA |
| contig00040 | 21860 | 22369 | (Tmt)dfrA20 | 0/0 | 100.0 | 100.0 | AJ605332:1304-1813 | (Tmt)dfrA20 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00060 | 1238 | 1771 | ant(2’’)-Ia | 0/0 | 100.0 | 100.0 | NG_047387.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig00025 | 23905 | 24693 | ant(3’’)-IIa | 0/0 | 100.0 | 100.0 | NG_054646.1 | aminoglycoside nucleotidyltransferase ANT(3’’)-IIa | SPECTINOMYCIN, STREPTOMYCIN |
| contig00052 | 3387 | 4214 | aph(3’’)-Ib | 0/0 | 100.0 | 99.9 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00060 | 372 | 1187 | aph(3’)-Ia | 0/0 | 100.0 | 100.0 | NG_047431.1 | aminoglycoside O-phosphotransferase APH(3’)-Ia | KANAMYCIN |
| contig00052 | 2551 | 3387 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00001 | 9 | 1160 | blaADC-30 | 0/0 | 100.0 | 100.0 | NG_048652.1 | class C extended-spectrum beta-lactamase ADC-30 | CEPHALOSPORIN |
| contig00027 | 47 | 889 | blaOXA-420 | 0/0 | 100.0 | 100.0 | NG_049708.1 | OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 | CARBAPENEM |
| contig00011 | 112601 | 113425 | blaOXA-69 | 0/0 | 100.0 | 100.0 | NG_049809.1 | OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69 | CARBAPENEM |
| contig00040 | 21860 | 22369 | dfrA20 | 0/0 | 100.0 | 100.0 | NG_047714.1 | trimethoprim-resistant dihydrofolate reductase DfrA20 | TRIMETHOPRIM |
| contig00027 | 5534 | 6418 | mph(E) | 0/0 | 100.0 | 100.0 | NG_064660.1 | Mph(E) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00027 | 6474 | 7949 | msr(E) | 0/0 | 100.0 | 100.0 | NG_048007.1 | ABC-F type ribosomal protection protein Msr(E) | MACROLIDE |
| contig00063 | 277 | 1089 | sul2 | 0/0 | 99.6 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00027 | 11112 | 12299 | tet(39) | 0/0 | 100.0 | 100.0 | NG_048137.1 | tetracycline efflux MFS transporter Tet(39) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00029 | 28006 | 29295 | ABAF | 0/0 | 100.0 | 97.9 | MEG_369 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF | NA |
| contig00012 | 20581 | 21885 | ABAQ | 0/0 | 100.0 | 100.0 | MEG_370 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ | NA |
| contig00006 | 14076 | 15422 | ABEM | 0/0 | 100.0 | 98.9 | MEG_372 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM | NA |
| contig00009 | 77409 | 77738 | ABES | 0/0 | 100.0 | 100.0 | MEG_379 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES | NA |
| contig00001 | 9 | 1160 | ADC | 0/0 | 100.0 | 100.0 | MEG_658 | Drugs:betalactams:Class_C_betalactamases:ADC | NA |
| contig00031 | 12186 | 13376 | ADEA | 0/0 | 100.0 | 97.7 | MEG_677 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA | NA |
| contig00031 | 9079 | 12186 | ADEB | 0/0 | 100.0 | 97.8 | MEG_678 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB | NA |
| contig00031 | 7605 | 9002 | ADEC | 0/0 | 100.0 | 95.4 | MEG_679 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEC | NA |
| contig00009 | 71651 | 72871 | ADEF | 0/0 | 100.0 | 100.0 | MEG_683 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEF | NA |
| contig00009 | 68465 | 71644 | ADEG | 0/0 | 100.0 | 100.0 | MEG_684 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG | NA |
| contig00009 | 67004 | 68455 | ADEH | 0/0 | 100.0 | 100.0 | MEG_685 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH | NA |
| contig00017 | 41693 | 42943 | ADEI | 0/0 | 100.0 | 100.0 | MEG_686 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI | NA |
| contig00017 | 42956 | 46132 | ADEJ | 0/0 | 100.0 | 99.6 | MEG_692 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ | NA |
| contig00017 | 46132 | 47586 | ADEK | 0/0 | 100.0 | 99.0 | MEG_696 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK | NA |
| contig00009 | 73087 | 74100 | ADEL | 0/0 | 100.0 | 99.5 | MEG_699 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL | NA |
| contig00008 | 75439 | 76092 | ADEN | 0/0 | 100.0 | 100.0 | MEG_701 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN | NA |
| contig00031 | 13522 | 14265 | ADER | 0/0 | 100.0 | 100.0 | MEG_703 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER | NA |
| contig00031 | 14297 | 15382 | ADES | 0/0 | 100.0 | 99.7 | MEG_704 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES | NA |
| contig00016 | 50011 | 50727 | ADET2 | 0/0 | 100.0 | 98.9 | MEG_706 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 | NA |
| contig00008 | 19900 | 21378 | AMVA | 0/0 | 100.0 | 100.0 | MEG_733 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA | NA |
| contig00025 | 23905 | 24693 | ANT3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_913 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00052 | 3387 | 4214 | APH3-DPRIME | 0/0 | 100.0 | 99.9 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00060 | 372 | 1187 | APH3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_1044 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00052 | 2551 | 3387 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00012 | 7956 | 8975 | BLAA | 0/0 | 100.0 | 99.9 | MEG_1246 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00022 | 41824 | 43098 | BLAA | 0/0 | 100.0 | 100.0 | MEG_1247 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00034 | 25919 | 26908 | MEXT | 0/0 | 100.0 | 98.8 | MEG_3934 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT | NA |
| contig00027 | 5534 | 6418 | MPHE | 0/0 | 100.0 | 100.0 | MEG_4044 | Drugs:MLS:Macrolide_phosphotransferases:MPHE | NA |
| contig00027 | 6474 | 7949 | MSRE | 0/0 | 100.0 | 100.0 | MEG_4075 | Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE | NA |
| contig00011 | 112556 | 113507 | OXA | 3/3 | 98.9 | 97.5 | MEG_5236 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00027 | 41 | 916 | OXA | 0/0 | 96.2 | 99.5 | MEG_5259 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00063 | 277 | 1089 | SULII | 0/0 | 99.6 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00027 | 11112 | 12299 | TET39 | 0/0 | 100.0 | 100.0 | MEG_6987 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00373 | 2685 | 3545 | aac(3)-IId_1 | 0/0 | 100.0 | 99.9 | EU022314 | aac(3)-IId | Gentamicin, Tobramycin |
| contig00373 | 1272 | 2074 | aph(3’’)-Ib_2 | 0/0 | 99.9 | 100.0 | AF024602 | aph(3’’)-Ib | Streptomycin |
| contig00373 | 436 | 1272 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00414 | 1262 | 2137 | blaCTX-M-15_1 | 0/0 | 100.0 | 100.0 | AY044436 | blaCTX-M-15 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig00473 | 93 | 905 | blaNDM-1_1 | 0/0 | 100.0 | 100.0 | FN396876 | blaNDM-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam |
| contig00052 | 35257 | 36087 | blaOXA-356_1 | 0/0 | 100.0 | 100.0 | KF297585 | blaOXA-356 | |
| contig00445 | 878 | 1720 | blaOXA-420_1 | 0/0 | 100.0 | 100.0 | AB983359 | blaOXA-420 | |
| contig00411 | 1004 | 1663 | catA1_1 | 0/0 | 100.0 | 99.8 | V00622 | catA1 | Chloramphenicol |
| contig00465 | 134 | 631 | dfrA12_8 | 0/0 | 100.0 | 100.0 | AM040708 | dfrA12 | Trimethoprim |
| contig00425 | 327 | 1540 | floR_2 | 0/0 | 99.9 | 98.3 | AF118107 | floR | Chloramphenicol, Florfenicol |
| contig00079 | 22839 | 24071 | mdf(A)_1 | 0/0 | 100.0 | 99.9 | Y08743 | mdf(A) | |
| contig00395 | 121 | 1005 | mph(E)_1 | 0/0 | 100.0 | 100.0 | DQ839391 | mph(E) | Erythromycin |
| contig00395 | 1061 | 2536 | msr(E)_1 | 0/0 | 100.0 | 100.0 | FR751518 | msr(E) | |
| contig00396 | 972 | 1838 | sul1_5 | 0/0 | 100.0 | 99.9 | EU780013 | sul1 | Sulfamethoxazole |
| contig00391 | 328 | 1143 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00424 | 82 | 1203 | tet(39)_1 | 0/0 | 100.0 | 99.9 | KT346360 | tet(39) | Doxycycline, Tetracycline |
| contig00394 | 948 | 2153 | tet(B)_2 | 0/0 | 100.0 | 100.0 | AF326777 | tet(B) | Doxycycline, Tetracycline, Minocycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00373 | 2685 | 3545 | AAC(3)-IId | 0/0 | 100.0 | 99.9 | EU022314.1:0-861 | AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli | aminoglycoside |
| contig00090 | 26373 | 29522 | acrB | 0/0 | 100.0 | 100.0 | U00096.3:484403-481253 | Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter. | cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00048 | 38923 | 42036 | acrD | 0/0 | 100.0 | 100.0 | AP009048.1:2586250-2589364 | AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. | aminoglycoside |
| contig00056 | 7448 | 8605 | acrE | 0/0 | 100.0 | 99.9 | U00096:3413863-3415021 | AcrE is a membrane fusion protein similar to AcrA. | cephalosporin, cephamycin, fluoroquinolone, penam |
| contig00056 | 4332 | 7436 | acrF | 0/0 | 100.0 | 99.9 | U00096:3415032-3418137 | AcrF is a inner membrane transporter similar to AcrB. | cephalosporin, cephamycin, fluoroquinolone, penam |
| contig00056 | 9004 | 9666 | acrS | 0/0 | 100.0 | 100.0 | U00096:3413465-3412802 | AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux. | cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00373 | 1272 | 2075 | APH(3’’)-Ib | 0/0 | 100.0 | 99.9 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00373 | 436 | 1272 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00374 | 1375 | 2196 | bacA | 0/0 | 100.0 | 98.7 | U00096.3:3204131-3203309 | The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. | peptide |
| contig00225 | 7328 | 8050 | baeR | 0/0 | 100.0 | 99.5 | AP009048.1:2166412-2167135 | BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. | aminocoumarin, aminoglycoside |
| contig00225 | 5928 | 7331 | baeS | 0/0 | 100.0 | 99.9 | AP009048:2165012-2166416 | BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance. | aminocoumarin, aminoglycoside |
| contig00411 | 1004 | 1663 | catI | 0/0 | 100.0 | 99.8 | V00622:243-903 | catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii | phenicol |
| contig00028 | 30399 | 31772 | cpxA | 0/0 | 100.0 | 99.0 | BA000007.3:4905062-4903688 | CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression. | aminocoumarin, aminoglycoside |
| contig00083 | 15080 | 15712 | CRP | 0/0 | 100.0 | 99.4 | AP009048.1:4154296-4153663 | CRP is a global regulator that represses MdtEF multidrug efflux pump expression. | fluoroquinolone, macrolide, penam |
| contig00414 | 1262 | 2137 | CTX-M-15 | 0/0 | 100.0 | 100.0 | AY044436:1435-2311 | CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family | cephalosporin |
| contig00473 | 909 | 1243 | determinant_of_bleomycin_resistance | 0/0 | 91.5 | 100.0 | KC503911.1:9883-10249 | A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. | glycopeptide |
| contig00465 | 134 | 631 | dfrA12 | 0/0 | 100.0 | 100.0 | GU585907.1:22103-21605 | dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae | diaminopyrimidine |
| contig00217 | 1578 | 2750 | emrA | 0/0 | 100.0 | 100.0 | AP009048:2810082-2811255 | EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium. | fluoroquinolone |
| contig00217 | 23 | 1561 | emrB | 0/0 | 100.0 | 100.0 | U00096:2812615-2814154 | emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin. | fluoroquinolone |
| contig00021 | 62059 | 63114 | emrK | 0/0 | 100.0 | 99.9 | D78168:536-1592 | emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux. | tetracycline |
| contig00217 | 2877 | 3407 | emrR | 0/0 | 100.0 | 99.8 | U00096.3:2810769-2811300 | EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. | fluoroquinolone |
| contig00021 | 60521 | 62059 | emrY | 0/0 | 100.0 | 99.9 | D78168:1591-3130 | emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB. | tetracycline |
| contig00101 | 7608 | 9251 | eptA | 0/0 | 100.0 | 99.9 | AP009048:4340268-4338624 | PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B. | peptide |
| contig00244 | 2156 | 3289 | Escherichia_coli_ampC | 0/0 | 100.0 | 97.3 | U00096.3:4378944-4377810 | A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics. | cephalosporin, penam |
| contig00125 | 17231 | 18535 | Escherichia_coli_ampC1_beta-lactamase | 0/0 | 100.0 | 99.9 | FN649414.1:2765050-2766355 | An ampC-like beta-lactamase identified from Escherichia coli. | cephalosporin, penam |
| contig00150 | 4921 | 6078 | Escherichia_coli_ampH | 0/0 | 100.0 | 100.0 | AP012030.1:396711-395553 | AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. | cephalosporin, penam |
| contig00079 | 22839 | 24071 | Escherichia_coli_mdfA | 0/0 | 100.0 | 98.4 | JQ394987:0-1233 | Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. | benzalkonium_chloride, rhodamine, tetracycline |
| contig00021 | 63637 | 64251 | evgA | 0/0 | 100.0 | 100.0 | BA000007.3:3212025-3212640 | EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed. | fluoroquinolone, macrolide, penam, tetracycline |
| contig00021 | 64256 | 67849 | evgS | 0/0 | 100.0 | 100.0 | U00096:2484373-2487967 | EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. | fluoroquinolone, macrolide, penam, tetracycline |
| contig00425 | 326 | 1540 | floR | 0/0 | 100.0 | 99.9 | AF231986:3307-4522 | floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae | phenicol |
| contig00067 | 1220 | 1948 | gadW | 0/0 | 100.0 | 94.7 | CP015085.1:2552440-2551711 | GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC. | fluoroquinolone, macrolide, penam |
| contig00067 | 29 | 853 | gadX | 0/0 | 100.0 | 100.0 | AP009048.1:3974604-3975429 | GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. | fluoroquinolone, macrolide, penam |
| contig00334 | 4348 | 4761 | H-NS | 0/0 | 100.0 | 99.3 | BA000007.3:1738104-1737690 | H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. | cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline |
| contig00084 | 7616 | 8293 | kdpE | 0/0 | 100.0 | 100.0 | U00096.3:721733-721055 | kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. | aminoglycoside |
| contig00242 | 1239 | 1622 | marA | 0/0 | 100.0 | 100.0 | AP009048.1:1621287-1621671 | In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF. | carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan |
| contig00377 | 554 | 1801 | mdtA | 0/0 | 100.0 | 98.0 | U00096:2154015-2155263 | MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. | aminocoumarin |
| contig00225 | 1438 | 4515 | mdtC | 0/0 | 100.0 | 99.9 | U00096:2158385-2161463 | MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58. | aminocoumarin |
| contig00067 | 5449 | 6606 | mdtE | 0/0 | 100.0 | 100.0 | AP009048.1:3981183-3980025 | MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. | fluoroquinolone, macrolide, penam |
| contig00067 | 2311 | 5424 | mdtF | 0/0 | 100.0 | 100.0 | U00096:3660413-3663527 | MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. | fluoroquinolone, macrolide, penam |
| contig00298 | 1763 | 2989 | mdtG | 0/0 | 100.0 | 99.3 | CP000800.1:1192954-1191727 | The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon. | fosfomycin |
| contig00306 | 3604 | 4812 | mdtH | 0/0 | 100.0 | 100.0 | U00096:1125326-1124117 | Multidrug resistance protein MdtH | fluoroquinolone |
| contig00100 | 473 | 1684 | mdtM | 0/0 | 98.3 | 95.5 | U00096.3:4568519-4567286 | Multidrug resistance protein MdtM | acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol |
| contig00114 | 17480 | 18511 | mdtN | 0/0 | 100.0 | 100.0 | AP009048.1:4307588-4306556 | Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. | acridine_dye, nucleoside |
| contig00114 | 15429 | 17480 | mdtO | 0/0 | 100.0 | 100.0 | AP009048.1:4306557-4304505 | Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride | acridine_dye, nucleoside |
| contig00114 | 13966 | 15432 | mdtP | 0/0 | 100.0 | 100.0 | AP009048.1:4304509-4303042 | Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride | acridine_dye, nucleoside |
| contig00048 | 17761 | 18237 | mphB | 0/0 | 100.0 | 98.3 | AE005174.2:3397370-3397847 | The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides. | macrolide |
| contig00395 | 121 | 1005 | mphE | 0/0 | 100.0 | 100.0 | DQ839391.1:13757-12872 | mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 | macrolide |
| contig00127 | 520 | 2268 | msbA | 0/0 | 100.0 | 100.0 | U00096.3:966620-968369 | MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability. | nitroimidazole |
| contig00395 | 1061 | 2536 | msrE | 0/0 | 100.0 | 100.0 | EU294228.1:21241-22717 | MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. | lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline |
| contig00473 | 93 | 905 | NDM-1 | 0/0 | 100.0 | 100.0 | FN396876:3219-2406 | NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. | carbapenem, cephalosporin, cephamycin, penam |
| contig00052 | 35257 | 36087 | OXA-356 | 0/0 | 100.0 | 100.0 | KF297585:0-831 | OXA-356 is a beta-lactamase. From the Lahey list of OXA beta-lactamases. | cephalosporin, penam |
| contig00445 | 878 | 1720 | OXA-420 | 0/0 | 100.0 | 100.0 | AB983359:2425-3268 | From the Lahey list of beta-lactamases. Not yet released. | cephalosporin, penam |
| contig00115 | 5199 | 6167 | pmrF | 0/0 | 100.0 | 100.0 | U00096:2367070-2368039 | PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. | peptide |
| contig00396 | 972 | 1811 | sul1 | 0/0 | 100.0 | 100.0 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig00391 | 328 | 1143 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00424 | 82 | 1269 | tet(39) | 0/0 | 100.0 | 99.9 | AY743590:0-1188 | Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. | tetracycline |
| contig00394 | 948 | 2153 | tet(B) | 0/0 | 100.0 | 99.8 | AB089595:0-1206 | Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline. | tetracycline |
| contig00069 | 15133 | 16620 | tolC | 0/0 | 100.0 | 99.7 | FJ768952:0-1488 | TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex. | aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan |
| contig00198 | 9354 | 10997 | yojI | 0/0 | 100.0 | 100.0 | U00096.3:2308615-2306971 | YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI. | peptide |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00373 | 2685 | 3545 | (AGly)aac3-IId | 0/0 | 100 | 99.9 | EU022314:1-861 | (AGly)aac3-IId | NA |
| contig00373 | 1272 | 2075 | (AGly)strA | 0/0 | 100 | 100.0 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00373 | 436 | 1272 | (AGly)strB | 0/0 | 100 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00125 | 17231 | 18535 | (Bla)AmpC1_Ecoli | 0/0 | 100 | 99.9 | FN649414:2765051-2766355 | (Bla)AmpC1_Ecoli | NA |
| contig00244 | 2156 | 3289 | (Bla)AmpC2_Ecoli | 0/0 | 100 | 97.3 | CP002970:332756-333889 | (Bla)AmpC2_Ecoli | NA |
| contig00150 | 4921 | 6078 | (Bla)ampH_Ecoli | 0/0 | 100 | 100.0 | AP012030:395554-396711 | (Bla)ampH_Ecoli | NA |
| contig00414 | 1262 | 2137 | (Bla)blaCTX-M-15 | 0/0 | 100 | 100.0 | JQ686199:261-1136 | (Bla)blaCTX-M-15 | NA |
| contig00473 | 93 | 905 | (Bla)blaNDM-1 | 0/0 | 100 | 100.0 | JQ080305:1-813 | (Bla)blaNDM-1 | NA |
| contig00052 | 35257 | 36087 | (Bla)blaOXA-230 | 0/0 | 100 | 99.0 | JQ422054:101-931 | (Bla)blaOXA-230 | NA |
| contig00445 | 878 | 1720 | (Bla)blaOXA-58 | 0/0 | 100 | 99.6 | AY665723:3301-4143 | (Bla)blaOXA-58 | NA |
| contig00258 | 5144 | 7045 | (Bla)Penicillin_Binding_Protein_Ecoli | 0/0 | 100 | 100.0 | CP002291:664439-666340 | (Bla)Penicillin_Binding_Protein_Ecoli | NA |
| contig00395 | 121 | 1005 | (MLS)mph(E) | 0/0 | 100 | 99.9 | JF769133:8777-9661 | (MLS)mph(E) | NA |
| contig00395 | 1061 | 2536 | (MLS)msr(E) | 0/0 | 100 | 100.0 | JF769133:7246-8721 | (MLS)msr(E) | NA |
| contig00411 | 1004 | 1663 | (Phe)catA1 | 0/0 | 100 | 99.8 | V00622:244-903 | (Phe)catA1 | NA |
| contig00425 | 326 | 1540 | (Phe)floR | 0/0 | 100 | 99.8 | AKLJ01000508:383-1597 | (Phe)floR | NA |
| contig00396 | 972 | 1811 | (Sul)sul1 | 0/0 | 100 | 100.0 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig00391 | 328 | 1143 | (Sul)sul2 | 0/0 | 100 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00424 | 82 | 1269 | (Tet)tet(39) | 0/0 | 100 | 99.9 | AY743590:749-1936 | (Tet)tet(39) | NA |
| contig00394 | 948 | 2153 | (Tet)tetB | 0/0 | 100 | 99.7 | AB089594:1-1206 | (Tet)tetB | NA |
| contig00465 | 134 | 631 | (Tmt)dfrA12 | 0/0 | 100 | 100.0 | Z21672:310-807 | (Tmt)dfrA12 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00373 | 2685 | 3545 | aac(3)-IId | 0/0 | 100.0 | 100.0 | NG_047251.1 | aminoglycoside N-acetyltransferase AAC(3)-IId | GENTAMICIN |
| contig00373 | 1272 | 2099 | aph(3’’)-Ib | 0/0 | 100.0 | 99.9 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00373 | 436 | 1272 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00414 | 1262 | 2137 | blaCTX-M-15 | 0/0 | 100.0 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00244 | 2156 | 3289 | blaEC-15 | 0/0 | 100.0 | 98.5 | NG_049081.1 | class C extended-spectrum beta-lactamase EC-15 | CEPHALOSPORIN |
| contig00473 | 93 | 905 | blaNDM-1 | 0/0 | 100.0 | 100.0 | NG_049326.1 | subclass B1 metallo-beta-lactamase NDM-1 | CARBAPENEM |
| contig00052 | 35257 | 36087 | blaOXA-356 | 0/0 | 100.0 | 100.0 | NG_049649.1 | OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-356 | CARBAPENEM |
| contig00445 | 878 | 1720 | blaOXA-420 | 0/0 | 100.0 | 100.0 | NG_049708.1 | OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 | CARBAPENEM |
| contig00473 | 909 | 1243 | ble-MBL | 0/0 | 91.5 | 100.0 | NG_047559.1 | bleomycin binding protein Ble-MBL | BLEOMYCIN |
| contig00411 | 1004 | 1663 | catA1 | 0/0 | 100.0 | 99.8 | NG_047582.1 | type A-1 chloramphenicol O-acetyltransferase | CHLORAMPHENICOL |
| contig00465 | 134 | 631 | dfrA12 | 0/0 | 100.0 | 100.0 | NG_047689.1 | trimethoprim-resistant dihydrofolate reductase DfrA12 | TRIMETHOPRIM |
| contig00425 | 326 | 1540 | floR | 0/0 | 100.0 | 100.0 | NG_047869.1 | chloramphenicol/florfenicol efflux MFS transporter FloR | CHLORAMPHENICOL, FLORFENICOL |
| contig00395 | 121 | 1005 | mph(E) | 0/0 | 100.0 | 100.0 | NG_064660.1 | Mph(E) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00395 | 1061 | 2536 | msr(E) | 0/0 | 100.0 | 100.0 | NG_048007.1 | ABC-F type ribosomal protection protein Msr(E) | MACROLIDE |
| contig00396 | 972 | 1811 | sul1 | 0/0 | 100.0 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| contig00391 | 328 | 1143 | sul2 | 0/0 | 100.0 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00424 | 82 | 1269 | tet(39) | 0/0 | 100.0 | 99.9 | NG_048137.1 | tetracycline efflux MFS transporter Tet(39) | TETRACYCLINE |
| contig00394 | 948 | 2153 | tet(B) | 0/0 | 100.0 | 100.0 | NG_048163.1 | tetracycline efflux MFS transporter Tet(B) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00373 | 2685 | 3545 | AAC3 | 0/0 | 100.0 | 100.0 | MEG_64 | Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 | NA |
| contig00090 | 26373 | 29522 | ACRB | 0/0 | 100.0 | 100.0 | MEG_401 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB | NA |
| contig00048 | 38923 | 42036 | ACRD | 0/0 | 100.0 | 100.0 | MEG_407 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD | NA |
| contig00056 | 7448 | 8605 | ACRE | 0/0 | 100.0 | 99.9 | MEG_408 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE | NA |
| contig00056 | 4332 | 7436 | ACRF | 0/0 | 100.0 | 99.9 | MEG_409 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF | NA |
| contig00056 | 9004 | 9666 | ACRS | 0/0 | 100.0 | 100.0 | MEG_415 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS | NA |
| contig00150 | 4921 | 6078 | AMPH | 0/0 | 100.0 | 100.0 | MEG_729 | Drugs:betalactams:Penicillin_binding_protein:AMPH | NA |
| contig00373 | 1272 | 2099 | APH3-DPRIME | 0/0 | 100.0 | 99.9 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00373 | 436 | 1272 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00156 | 2787 | 4639 | ASMA | 0/0 | 100.0 | 97.2 | MEG_1180 | Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA | NA |
| contig00374 | 1375 | 2196 | BACA | 0/0 | 100.0 | 98.9 | MEG_1189 | Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA | NA |
| contig00225 | 7328 | 8050 | BAER | 0/0 | 100.0 | 99.5 | MEG_1192 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER | NA |
| contig00225 | 5928 | 7331 | BAES | 0/0 | 100.0 | 99.9 | MEG_1193 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES | NA |
| contig00080 | 9933 | 11123 | BCR | 0/0 | 100.0 | 99.9 | MEG_1210 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR | NA |
| contig00244 | 2156 | 3289 | BLAEC | 0/0 | 100.0 | 98.5 | MEG_1282 | Drugs:betalactams:Class_C_betalactamases:BLAEC | NA |
| contig00473 | 909 | 1243 | BRP | 0/0 | 91.5 | 100.0 | MEG_1477 | Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP | NA |
| contig00411 | 999 | 1663 | CATA | 0/0 | 99.1 | 100.0 | MEG_1593 | Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA | NA |
| contig00028 | 29704 | 30402 | CPXAR | 0/0 | 100.0 | 100.0 | MEG_2122 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR | NA |
| contig00028 | 30399 | 31772 | CPXAR | 0/0 | 100.0 | 100.0 | MEG_2121 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR | NA |
| contig00083 | 15080 | 15712 | CRP | 0/0 | 100.0 | 99.4 | MEG_2132 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP | NA |
| contig00160 | 13705 | 14647 | CTX | 0/0 | 100.0 | 98.2 | MEG_2435 | Drugs:betalactams:Class_A_betalactamases:CTX | NA |
| contig00465 | 134 | 631 | DFRA | 0/0 | 100.0 | 100.0 | MEG_2551 | Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA | NA |
| contig00217 | 1578 | 2750 | EMRA | 0/0 | 100.0 | 100.0 | MEG_2722 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA | NA |
| contig00217 | 23 | 1561 | EMRB | 0/0 | 100.0 | 100.0 | MEG_2725 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB | NA |
| contig00120 | 19649 | 20839 | EMRD | 0/0 | 100.0 | 99.9 | MEG_2729 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD | NA |
| contig00021 | 62059 | 63222 | EMRK | 0/0 | 100.0 | 99.9 | MEG_2732 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK | NA |
| contig00217 | 2877 | 3407 | EMRR | 0/0 | 100.0 | 99.8 | MEG_2734 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR | NA |
| contig00021 | 60521 | 62059 | EMRY | 0/0 | 100.0 | 99.9 | MEG_2736 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY | NA |
| contig00101 | 7608 | 9251 | EPTA | 0/0 | 100.0 | 99.9 | MEG_2739 | Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA | NA |
| contig00021 | 64256 | 67849 | EVGS | 0/0 | 100.0 | 100.0 | MEG_2870 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS | NA |
| contig00425 | 326 | 1540 | FLOR | 0/0 | 100.0 | 100.0 | MEG_2923 | Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR | NA |
| contig00067 | 1220 | 1948 | GADW | 0/0 | 100.0 | 100.0 | MEG_3081 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW | NA |
| contig00067 | 29 | 853 | GADX | 0/0 | 100.0 | 100.0 | MEG_3083 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX | NA |
| contig00334 | 4348 | 4761 | HNS | 0/0 | 100.0 | 99.3 | MEG_3271 | Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS | NA |
| contig00084 | 7616 | 8293 | KDPE | 0/0 | 100.0 | 100.0 | MEG_3448 | Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE | NA |
| contig00242 | 1233 | 1622 | MARA | 0/0 | 100.0 | 100.0 | MEG_3662 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA | NA |
| contig00242 | 785 | 1219 | MARR | 0/0 | 100.0 | 100.0 | MEG_3663 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR | NA |
| contig00079 | 22839 | 24071 | MDFA | 0/0 | 100.0 | 100.0 | MEG_3737 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA | NA |
| contig00377 | 554 | 1801 | MDTA | 0/0 | 100.0 | 98.0 | MEG_3746 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA | NA |
| contig00225 | 1438 | 4515 | MDTC | 0/0 | 100.0 | 99.9 | MEG_3749 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC | NA |
| contig00067 | 5449 | 6606 | MDTE | 0/0 | 100.0 | 100.0 | MEG_3751 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE | NA |
| contig00067 | 2311 | 5424 | MDTF | 0/0 | 100.0 | 100.0 | MEG_3752 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF | NA |
| contig00298 | 1763 | 2989 | MDTG | 0/0 | 100.0 | 99.9 | MEG_3753 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG | NA |
| contig00306 | 3604 | 4812 | MDTH | 0/0 | 100.0 | 100.0 | MEG_3755 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH | NA |
| contig00043 | 23790 | 24119 | MDTI | 0/0 | 100.0 | 100.0 | MEG_3756 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI | NA |
| contig00043 | 24106 | 24471 | MDTJ | 0/0 | 100.0 | 99.5 | MEG_3757 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ | NA |
| contig00182 | 11709 | 13082 | MDTK | 0/0 | 100.0 | 100.0 | MEG_3759 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK | NA |
| contig00100 | 473 | 1684 | MDTM | 0/0 | 98.3 | 95.5 | MEG_3761 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM | NA |
| contig00114 | 17480 | 18511 | MDTN | 0/0 | 100.0 | 100.0 | MEG_3763 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN | NA |
| contig00114 | 15429 | 17480 | MDTO | 0/0 | 100.0 | 100.0 | MEG_3764 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO | NA |
| contig00114 | 13966 | 15432 | MDTP | 0/0 | 100.0 | 100.0 | MEG_3765 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP | NA |
| contig00048 | 17761 | 18237 | MPHB | 0/0 | 100.0 | 98.3 | MEG_4033 | Drugs:MLS:Macrolide_phosphotransferases:MPHB | NA |
| contig00395 | 121 | 1005 | MPHE | 0/0 | 100.0 | 100.0 | MEG_4044 | Drugs:MLS:Macrolide_phosphotransferases:MPHE | NA |
| contig00127 | 520 | 2268 | MSBA | 0/0 | 100.0 | 100.0 | MEG_4061 | Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA | NA |
| contig00395 | 1061 | 2536 | MSRE | 0/0 | 100.0 | 100.0 | MEG_4075 | Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE | NA |
| contig00473 | 93 | 905 | NDM | 0/0 | 100.0 | 100.0 | MEG_4143 | Drugs:betalactams:Class_B_betalactamases:NDM | NA |
| contig00052 | 35222 | 36187 | OXA | 0/0 | 100.0 | 98.9 | MEG_5220 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00445 | 872 | 1742 | OXA | 0/0 | 95.6 | 99.5 | MEG_5259 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00258 | 5144 | 7045 | PBP2 | 0/0 | 100.0 | 100.0 | MEG_5400 | Drugs:betalactams:Penicillin_binding_protein:PBP2 | NA |
| contig00125 | 17231 | 18535 | PBP4B | 0/0 | 100.0 | 99.9 | MEG_5409 | Drugs:betalactams:Penicillin_binding_protein:PBP4B | NA |
| contig00115 | 5199 | 6167 | PMRF | 0/0 | 100.0 | 100.0 | MEG_5801 | Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF | NA |
| contig00065 | 2810 | 3679 | ROBA | 0/0 | 100.0 | 99.0 | MEG_6082 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA | NA |
| contig00238 | 2432 | 2755 | SOXS | 0/0 | 100.0 | 100.0 | MEG_6551 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS | NA |
| contig00396 | 845 | 1812 | SULI | 0/0 | 100.0 | 100.0 | MEG_6615 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI | NA |
| contig00391 | 328 | 1143 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00424 | 82 | 1269 | TET39 | 0/0 | 100.0 | 99.9 | MEG_6987 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 | NA |
| contig00394 | 948 | 2153 | TETB | 0/0 | 100.0 | 100.0 | MEG_7052 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB | NA |
| contig00198 | 9354 | 10997 | YOGI | 0/0 | 100.0 | 100.0 | MEG_7842 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00231 | 4721 | 5254 | ant(2’’)-Ia_13 | 0/0 | 100.0 | 99.1 | DQ176450 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00184 | 6719 | 7521 | aph(3’’)-Ib_2 | 0/0 | 99.9 | 100.0 | AF024602 | aph(3’’)-Ib | Streptomycin |
| contig00184 | 5883 | 6719 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00968 | 92 | 904 | blaNDM-1_1 | 0/0 | 100.0 | 100.0 | FN396876 | blaNDM-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam |
| contig00614 | 1050 | 1874 | blaOXA-22_1 | 0/0 | 100.0 | 100.0 | AF064820 | blaOXA-22 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig00525 | 254 | 1096 | blaOXA-420_1 | 0/0 | 100.0 | 100.0 | AB983359 | blaOXA-420 | |
| contig01193 | 1 | 803 | blaOXA-60_1 | 0/0 | 98.4 | 100.0 | AF525303 | blaOXA-60 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Imipenem |
| contig01103 | 503 | 1318 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00231 | 4721 | 5254 | ANT(2’’)-Ia | 0/0 | 100.0 | 98.9 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig00184 | 6719 | 7522 | APH(3’’)-Ib | 0/0 | 100.0 | 99.9 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00184 | 5883 | 6719 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00968 | 908 | 1273 | determinant_of_bleomycin_resistance | 0/0 | 100.0 | 100.0 | KC503911.1:9883-10249 | A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. | glycopeptide |
| contig00968 | 92 | 904 | NDM-1 | 0/0 | 100.0 | 100.0 | FN396876:3219-2406 | NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. | carbapenem, cephalosporin, cephamycin, penam |
| contig00614 | 1050 | 1874 | OXA-22 | 0/0 | 100.0 | 100.0 | AF064820:951-1776 | OXA-22 is a beta-lactamase found in Ralstonia pickettii | cephalosporin, penam |
| contig00525 | 254 | 1096 | OXA-420 | 0/0 | 100.0 | 100.0 | AB983359:2425-3268 | From the Lahey list of beta-lactamases. Not yet released. | cephalosporin, penam |
| contig01193 | 1 | 803 | OXA-60 | 0/0 | 98.4 | 100.0 | AF525303:2770-3586 | OXA-60 is a beta-lactamase found in Ralstonia pickettii | cephalosporin, penam |
| contig01103 | 503 | 1318 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00231 | 4721 | 5254 | (AGly)aadB | 0/0 | 100.0 | 98.9 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig00184 | 6719 | 7522 | (AGly)strA | 0/0 | 100.0 | 100.0 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00184 | 5883 | 6719 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00968 | 92 | 904 | (Bla)blaNDM-1 | 0/0 | 100.0 | 100.0 | JQ080305:1-813 | (Bla)blaNDM-1 | NA |
| contig00614 | 1050 | 1874 | (Bla)blaOXA-22 | 0/0 | 100.0 | 100.0 | AF064820:952-1776 | (Bla)blaOXA-22 | NA |
| contig00525 | 254 | 1096 | (Bla)blaOXA-58 | 0/0 | 100.0 | 99.6 | AY665723:3301-4143 | (Bla)blaOXA-58 | NA |
| contig01193 | 3 | 803 | (Bla)blaOXA-60 | 0/0 | 98.2 | 93.5 | AY664505:1-816 | (Bla)blaOXA-60 | NA |
| contig01103 | 503 | 1318 | (Sul)sul2 | 0/0 | 100.0 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00231 | 4721 | 5254 | ant(2’’)-Ia | 0/0 | 100.0 | 99.1 | NG_052432.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig00184 | 6719 | 7546 | aph(3’’)-Ib | 0/0 | 100.0 | 99.9 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00184 | 5883 | 6719 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00968 | 92 | 904 | blaNDM-1 | 0/0 | 100.0 | 100.0 | NG_049326.1 | subclass B1 metallo-beta-lactamase NDM-1 | CARBAPENEM |
| contig00614 | 1050 | 1874 | blaOXA-22 | 0/0 | 100.0 | 100.0 | NG_049518.1 | benzylpenicillin-hydrolyzing class D beta-lactamase OXA-22 | BETA-LACTAM |
| contig00525 | 254 | 1096 | blaOXA-420 | 0/0 | 100.0 | 100.0 | NG_049708.1 | OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 | CARBAPENEM |
| contig01193 | 1 | 803 | blaOXA-60 | 0/0 | 98.4 | 100.0 | NG_049800.1 | carbapenem-hydrolyzing class D beta-lactamase OXA-60 | CARBAPENEM |
| contig00968 | 908 | 1273 | ble-MBL | 0/0 | 100.0 | 100.0 | NG_047559.1 | bleomycin binding protein Ble-MBL | BLEOMYCIN |
| contig01103 | 503 | 1318 | sul2 | 0/0 | 100.0 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00184 | 6719 | 7546 | APH3-DPRIME | 0/0 | 100.0 | 99.9 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00184 | 5883 | 6719 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00968 | 908 | 1273 | BRP | 0/0 | 100.0 | 100.0 | MEG_1477 | Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP | NA |
| contig00968 | 92 | 904 | NDM | 0/0 | 100.0 | 100.0 | MEG_4143 | Drugs:betalactams:Class_B_betalactamases:NDM | NA |
| contig00525 | 227 | 1102 | OXA | 0/0 | 96.2 | 99.5 | MEG_5259 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00614 | 1050 | 1874 | OXA | 0/0 | 100.0 | 100.0 | MEG_4766 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig01193 | 1 | 803 | OXA | 0/0 | 98.4 | 100.0 | MEG_4779 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig01103 | 503 | 1318 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00046 | 23105 | 23908 | aph(3’’)-Ib_5 | 0/0 | 100.0 | 100.0 | AF321551 | aph(3’’)-Ib | Streptomycin |
| contig00046 | 22269 | 23105 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00046 | 16991 | 17866 | blaCTX-M-15_1 | 0/0 | 100.0 | 100.0 | AY044436 | blaCTX-M-15 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig00046 | 20688 | 21548 | blaTEM-1B_1 | 0/0 | 100.0 | 100.0 | AY458016 | blaTEM-1B | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin |
| contig00086 | 182 | 664 | dfrA14_5 | 0/0 | 100.0 | 99.6 | DQ388123 | dfrA14 | Trimethoprim |
| contig00044 | 26094 | 27326 | mdf(A)_1 | 0/0 | 100.0 | 99.9 | Y08743 | mdf(A) | |
| contig00046 | 11694 | 12350 | qnrS1_1 | 0/0 | 100.0 | 100.0 | AB187515 | qnrS1 | Ciprofloxacin |
| contig00046 | 23969 | 24784 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00072 | 2413 | 3659 | tet(A)_6 | 0/0 | 97.8 | 100.0 | AF534183 | tet(A) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00008 | 39911 | 43060 | acrB | 0/0 | 100.0 | 100.0 | U00096.3:484403-481253 | Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter. | cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00001 | 264252 | 267365 | acrD | 0/0 | 100.0 | 100.0 | AP009048.1:2586250-2589364 | AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. | aminoglycoside |
| contig00033 | 8847 | 10004 | acrE | 0/0 | 100.0 | 100.0 | U00096:3413863-3415021 | AcrE is a membrane fusion protein similar to AcrA. | cephalosporin, cephamycin, fluoroquinolone, penam |
| contig00033 | 5731 | 8835 | acrF | 0/0 | 100.0 | 99.5 | U00096:3415032-3418137 | AcrF is a inner membrane transporter similar to AcrB. | cephalosporin, cephamycin, fluoroquinolone, penam |
| contig00033 | 10403 | 11065 | acrS | 0/0 | 100.0 | 100.0 | U00096:3413465-3412802 | AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux. | cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00046 | 23105 | 23908 | APH(3’’)-Ib | 0/0 | 100.0 | 99.8 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00046 | 22269 | 23105 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00043 | 29802 | 30623 | bacA | 0/0 | 100.0 | 100.0 | U00096.3:3204131-3203309 | The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. | peptide |
| contig00002 | 136446 | 137168 | baeR | 0/0 | 100.0 | 100.0 | AP009048.1:2166412-2167135 | BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. | aminocoumarin, aminoglycoside |
| contig00002 | 137165 | 138568 | baeS | 0/0 | 100.0 | 100.0 | AP009048:2165012-2166416 | BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance. | aminocoumarin, aminoglycoside |
| contig00037 | 2729 | 4102 | cpxA | 0/0 | 100.0 | 99.0 | BA000007.3:4905062-4903688 | CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression. | aminocoumarin, aminoglycoside |
| contig00045 | 15323 | 15955 | CRP | 0/0 | 100.0 | 99.4 | AP009048.1:4154296-4153663 | CRP is a global regulator that represses MdtEF multidrug efflux pump expression. | fluoroquinolone, macrolide, penam |
| contig00046 | 16991 | 17866 | CTX-M-15 | 0/0 | 100.0 | 100.0 | AY044436:1435-2311 | CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family | cephalosporin |
| contig00086 | 182 | 664 | dfrA14 | 0/0 | 100.0 | 99.8 | EU780012:2162-2645 | dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli | diaminopyrimidine |
| contig00010 | 80125 | 81297 | emrA | 0/0 | 100.0 | 99.9 | AP009048:2810082-2811255 | EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium. | fluoroquinolone |
| contig00010 | 81314 | 82852 | emrB | 0/0 | 100.0 | 99.8 | U00096:2812615-2814154 | emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin. | fluoroquinolone |
| contig00001 | 167043 | 168098 | emrK | 0/0 | 100.0 | 99.9 | D78168:536-1592 | emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux. | tetracycline |
| contig00010 | 79468 | 79998 | emrR | 0/0 | 100.0 | 100.0 | U00096.3:2810769-2811300 | EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. | fluoroquinolone |
| contig00001 | 165505 | 167043 | emrY | 0/0 | 100.0 | 99.0 | D78168:1591-3130 | emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB. | tetracycline |
| contig00048 | 7625 | 9268 | eptA | 0/0 | 100.0 | 100.0 | AP009048:4340268-4338624 | PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B. | peptide |
| contig00008 | 38695 | 39888 | Escherichia_coli_acrA | 0/0 | 100.0 | 100.0 | U00096.3:485619-484425 | AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli. | cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00034 | 38142 | 39275 | Escherichia_coli_ampC | 0/0 | 100.0 | 97.3 | U00096.3:4378944-4377810 | A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics. | cephalosporin, penam |
| contig00001 | 231621 | 232925 | Escherichia_coli_ampC1_beta-lactamase | 0/0 | 100.0 | 99.9 | FN649414.1:2765050-2766355 | An ampC-like beta-lactamase identified from Escherichia coli. | cephalosporin, penam |
| contig00006 | 894 | 2051 | Escherichia_coli_ampH | 0/0 | 100.0 | 98.8 | AP012030.1:396711-395553 | AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. | cephalosporin, penam |
| contig00044 | 26094 | 27326 | Escherichia_coli_mdfA | 0/0 | 100.0 | 98.4 | JQ394987:0-1233 | Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. | benzalkonium_chloride, rhodamine, tetracycline |
| contig00001 | 168622 | 169236 | evgA | 0/0 | 100.0 | 100.0 | BA000007.3:3212025-3212640 | EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed. | fluoroquinolone, macrolide, penam, tetracycline |
| contig00001 | 169241 | 172834 | evgS | 0/0 | 100.0 | 99.7 | U00096:2484373-2487967 | EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. | fluoroquinolone, macrolide, penam, tetracycline |
| contig00007 | 97645 | 98373 | gadW | 0/0 | 100.0 | 94.7 | CP015085.1:2552440-2551711 | GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC. | fluoroquinolone, macrolide, penam |
| contig00007 | 96453 | 97277 | gadX | 0/0 | 100.0 | 100.0 | AP009048.1:3974604-3975429 | GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. | fluoroquinolone, macrolide, penam |
| contig00004 | 161513 | 161926 | H-NS | 0/0 | 100.0 | 99.5 | BA000007.3:1738104-1737690 | H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. | cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline |
| contig00012 | 8068 | 8745 | kdpE | 0/0 | 100.0 | 100.0 | U00096.3:721733-721055 | kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. | aminoglycoside |
| contig00015 | 88557 | 88940 | marA | 0/0 | 100.0 | 99.7 | AP009048.1:1621287-1621671 | In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF. | carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan |
| contig00002 | 146181 | 147428 | mdtA | 0/0 | 100.0 | 99.5 | U00096:2154015-2155263 | MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. | aminocoumarin |
| contig00002 | 143059 | 146181 | mdtB | 0/0 | 100.0 | 98.7 | U00096:2155262-2158385 | MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. | aminocoumarin |
| contig00002 | 139981 | 143058 | mdtC | 0/0 | 100.0 | 99.8 | U00096:2158385-2161463 | MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58. | aminocoumarin |
| contig00007 | 101874 | 103031 | mdtE | 0/0 | 100.0 | 100.0 | AP009048.1:3981183-3980025 | MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. | fluoroquinolone, macrolide, penam |
| contig00007 | 98736 | 101849 | mdtF | 0/0 | 100.0 | 100.0 | U00096:3660413-3663527 | MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. | fluoroquinolone, macrolide, penam |
| contig00005 | 163790 | 165016 | mdtG | 0/0 | 100.0 | 99.4 | CP000800.1:1192954-1191727 | The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon. | fosfomycin |
| contig00004 | 8504 | 9712 | mdtH | 0/0 | 100.0 | 99.8 | U00096:1125326-1124117 | Multidrug resistance protein MdtH | fluoroquinolone |
| contig00050 | 473 | 1684 | mdtM | 0/0 | 98.3 | 95.6 | U00096.3:4568519-4567286 | Multidrug resistance protein MdtM | acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol |
| contig00016 | 6677 | 7708 | mdtN | 0/0 | 100.0 | 100.0 | AP009048.1:4307588-4306556 | Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. | acridine_dye, nucleoside |
| contig00016 | 7708 | 9759 | mdtO | 0/0 | 100.0 | 100.0 | AP009048.1:4306557-4304505 | Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride | acridine_dye, nucleoside |
| contig00016 | 9756 | 11222 | mdtP | 0/0 | 100.0 | 100.0 | AP009048.1:4304509-4303042 | Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride | acridine_dye, nucleoside |
| contig00001 | 287883 | 288357 | mphB | 0/0 | 99.6 | 97.3 | AE005174.2:3397370-3397847 | The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides. | macrolide |
| contig00005 | 17130 | 18878 | msbA | 0/0 | 100.0 | 100.0 | U00096.3:966620-968369 | MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability. | nitroimidazole |
| contig00001 | 62154 | 63122 | pmrF | 0/0 | 100.0 | 100.0 | U00096:2367070-2368039 | PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. | peptide |
| contig00046 | 11694 | 12350 | QnrS1 | 0/0 | 100.0 | 100.0 | DQ485529.1:0-657 | QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri | fluoroquinolone |
| contig00046 | 23969 | 24784 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00046 | 20688 | 21548 | TEM-1 | 0/0 | 100.0 | 99.9 | AL513383:161910-162771 | TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. | cephalosporin, monobactam, penam, penem |
| contig00072 | 2413 | 3659 | tet(A) | 0/0 | 97.8 | 100.0 | AF534183.1:2970-4245 | TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. | tetracycline |
| contig00043 | 5937 | 7424 | tolC | 0/0 | 100.0 | 99.7 | FJ768952:0-1488 | TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex. | aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan |
| contig00001 | 2055 | 3698 | yojI | 0/0 | 100.0 | 100.0 | U00096.3:2308615-2306971 | YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI. | peptide |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00046 | 23105 | 23908 | (AGly)strA | 0/0 | 100 | 99.9 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00046 | 22269 | 23105 | (AGly)strB | 0/0 | 100 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00001 | 231621 | 232925 | (Bla)AmpC1_Ecoli | 0/0 | 100 | 99.9 | FN649414:2765051-2766355 | (Bla)AmpC1_Ecoli | NA |
| contig00034 | 38142 | 39275 | (Bla)AmpC2_Ecoli | 0/0 | 100 | 97.3 | CP002970:332756-333889 | (Bla)AmpC2_Ecoli | NA |
| contig00006 | 894 | 2051 | (Bla)ampH_Ecoli | 0/0 | 100 | 98.8 | AP012030:395554-396711 | (Bla)ampH_Ecoli | NA |
| contig00046 | 16991 | 17866 | (Bla)blaCTX-M-15 | 0/0 | 100 | 100.0 | JQ686199:261-1136 | (Bla)blaCTX-M-15 | NA |
| contig00046 | 20688 | 21548 | (Bla)blaTEM-105 | 0/0 | 100 | 99.9 | AF516720:215-1075 | (Bla)blaTEM-105 | NA |
| contig00012 | 60449 | 62350 | (Bla)Penicillin_Binding_Protein_Ecoli | 0/0 | 100 | 100.0 | CP002291:664439-666340 | (Bla)Penicillin_Binding_Protein_Ecoli | NA |
| contig00046 | 11694 | 12350 | (Flq)qnr-S1 | 0/0 | 100 | 100.0 | AB187515:9737-10393 | (Flq)qnr-S1 | NA |
| contig00046 | 23969 | 24784 | (Sul)sul2 | 0/0 | 100 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00072 | 2385 | 3659 | (Tet)tetA | 0/0 | 100 | 100.0 | JX424423:94438-95712 | (Tet)tetA | NA |
| contig00072 | 3690 | 4340 | (Tet)tetR | 0/0 | 100 | 100.0 | HF545434:53576-54226 | (Tet)tetR | NA |
| contig00086 | 182 | 655 | (Tmt)dfrA14 | 0/0 | 100 | 100.0 | GU726917:72-545 | (Tmt)dfrA14 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00046 | 23105 | 23932 | aph(3’’)-Ib | 0/0 | 100 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00046 | 22269 | 23105 | aph(6)-Id | 0/0 | 100 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00046 | 16991 | 17866 | blaCTX-M-15 | 0/0 | 100 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00034 | 38142 | 39275 | blaEC-15 | 0/0 | 100 | 98.6 | NG_049081.1 | class C extended-spectrum beta-lactamase EC-15 | CEPHALOSPORIN |
| contig00046 | 20688 | 21548 | blaTEM-1 | 0/0 | 100 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00086 | 182 | 655 | dfrA14 | 0/0 | 100 | 100.0 | NG_056035.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | TRIMETHOPRIM |
| contig00046 | 11694 | 12350 | qnrS1 | 0/0 | 100 | 100.0 | NG_050543.1 | quinolone resistance pentapeptide repeat protein QnrS1 | QUINOLONE |
| contig00046 | 23969 | 24784 | sul2 | 0/0 | 100 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00072 | 2385 | 3584 | tet(A) | 0/0 | 100 | 100.0 | NG_048154.1 | tetracycline efflux MFS transporter Tet(A) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00008 | 38695 | 39888 | ACRA | 0/0 | 100.0 | 100.0 | MEG_399 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA | NA |
| contig00008 | 39911 | 43060 | ACRB | 0/0 | 100.0 | 100.0 | MEG_401 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB | NA |
| contig00001 | 264252 | 267365 | ACRD | 0/0 | 100.0 | 100.0 | MEG_407 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD | NA |
| contig00033 | 8847 | 10004 | ACRE | 0/0 | 100.0 | 100.0 | MEG_408 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE | NA |
| contig00033 | 5731 | 8835 | ACRF | 0/0 | 100.0 | 99.5 | MEG_409 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF | NA |
| contig00033 | 10403 | 11065 | ACRS | 0/0 | 100.0 | 100.0 | MEG_415 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS | NA |
| contig00006 | 894 | 2051 | AMPH | 0/0 | 100.0 | 98.8 | MEG_729 | Drugs:betalactams:Penicillin_binding_protein:AMPH | NA |
| contig00046 | 23105 | 23932 | APH3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00046 | 22269 | 23105 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00002 | 159831 | 161683 | ASMA | 0/0 | 100.0 | 98.1 | MEG_1180 | Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA | NA |
| contig00043 | 29802 | 30623 | BACA | 0/0 | 100.0 | 100.0 | MEG_1190 | Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA | NA |
| contig00002 | 136446 | 137168 | BAER | 0/0 | 100.0 | 100.0 | MEG_1192 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER | NA |
| contig00002 | 137165 | 138568 | BAES | 0/0 | 100.0 | 100.0 | MEG_1193 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES | NA |
| contig00002 | 23573 | 24763 | BCR | 0/0 | 100.0 | 100.0 | MEG_1210 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR | NA |
| contig00034 | 38142 | 39275 | BLAEC | 0/0 | 100.0 | 98.6 | MEG_1282 | Drugs:betalactams:Class_C_betalactamases:BLAEC | NA |
| contig00037 | 2034 | 2732 | CPXAR | 0/0 | 100.0 | 100.0 | MEG_2122 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR | NA |
| contig00037 | 2729 | 4102 | CPXAR | 0/0 | 100.0 | 100.0 | MEG_2121 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR | NA |
| contig00045 | 15323 | 15955 | CRP | 0/0 | 100.0 | 99.4 | MEG_2132 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP | NA |
| contig00086 | 182 | 655 | DFRA | 0/0 | 100.0 | 99.8 | MEG_2517 | Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA | NA |
| contig00010 | 80125 | 81297 | EMRA | 0/0 | 100.0 | 99.9 | MEG_2722 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA | NA |
| contig00010 | 81314 | 82852 | EMRB | 0/0 | 100.0 | 99.8 | MEG_2725 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB | NA |
| contig00056 | 16852 | 18042 | EMRD | 0/0 | 100.0 | 100.0 | MEG_2729 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD | NA |
| contig00001 | 167043 | 168206 | EMRK | 0/0 | 100.0 | 99.9 | MEG_2732 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK | NA |
| contig00010 | 79468 | 79998 | EMRR | 0/0 | 100.0 | 100.0 | MEG_2734 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR | NA |
| contig00001 | 165505 | 167043 | EMRY | 0/0 | 100.0 | 99.1 | MEG_2736 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY | NA |
| contig00048 | 7625 | 9268 | EPTA | 0/0 | 100.0 | 100.0 | MEG_2739 | Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA | NA |
| contig00001 | 169241 | 172834 | EVGS | 0/0 | 100.0 | 99.7 | MEG_2870 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS | NA |
| contig00007 | 97645 | 98373 | GADW | 0/0 | 100.0 | 100.0 | MEG_3081 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW | NA |
| contig00007 | 96453 | 97277 | GADX | 0/0 | 100.0 | 100.0 | MEG_3083 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX | NA |
| contig00004 | 161513 | 161926 | HNS | 0/0 | 100.0 | 99.5 | MEG_3271 | Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS | NA |
| contig00012 | 8068 | 8745 | KDPE | 0/0 | 100.0 | 100.0 | MEG_3448 | Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE | NA |
| contig00015 | 88551 | 88940 | MARA | 0/0 | 100.0 | 99.7 | MEG_3662 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA | NA |
| contig00015 | 88102 | 88536 | MARR | 0/0 | 100.0 | 98.4 | MEG_3663 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR | NA |
| contig00044 | 26094 | 27326 | MDFA | 0/0 | 100.0 | 100.0 | MEG_3737 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA | NA |
| contig00002 | 146181 | 147428 | MDTA | 0/0 | 100.0 | 99.5 | MEG_3746 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA | NA |
| contig00002 | 143059 | 146181 | MDTB | 0/0 | 100.0 | 98.7 | MEG_3747 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB | NA |
| contig00002 | 139981 | 143058 | MDTC | 0/0 | 100.0 | 99.8 | MEG_3749 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC | NA |
| contig00007 | 101874 | 103031 | MDTE | 0/0 | 100.0 | 100.0 | MEG_3751 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE | NA |
| contig00007 | 98736 | 101849 | MDTF | 0/0 | 100.0 | 100.0 | MEG_3752 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF | NA |
| contig00005 | 163790 | 165016 | MDTG | 0/0 | 100.0 | 100.0 | MEG_3753 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG | NA |
| contig00004 | 8504 | 9712 | MDTH | 0/0 | 100.0 | 99.8 | MEG_3755 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH | NA |
| contig00003 | 220698 | 221027 | MDTI | 0/0 | 100.0 | 100.0 | MEG_3756 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI | NA |
| contig00003 | 220346 | 220711 | MDTJ | 0/0 | 100.0 | 99.5 | MEG_3757 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ | NA |
| contig00003 | 148945 | 150318 | MDTK | 0/0 | 100.0 | 99.9 | MEG_3759 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK | NA |
| contig00050 | 473 | 1684 | MDTM | 0/0 | 98.3 | 95.6 | MEG_3761 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM | NA |
| contig00016 | 6677 | 7708 | MDTN | 0/0 | 100.0 | 100.0 | MEG_3763 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN | NA |
| contig00016 | 7708 | 9759 | MDTO | 0/0 | 100.0 | 100.0 | MEG_3764 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO | NA |
| contig00016 | 9756 | 11222 | MDTP | 0/0 | 100.0 | 100.0 | MEG_3765 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP | NA |
| contig00001 | 287883 | 288357 | MPHB | 0/0 | 99.6 | 97.3 | MEG_4033 | Drugs:MLS:Macrolide_phosphotransferases:MPHB | NA |
| contig00005 | 17130 | 18878 | MSBA | 0/0 | 100.0 | 100.0 | MEG_4061 | Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA | NA |
| contig00012 | 60449 | 62350 | PBP2 | 0/0 | 100.0 | 100.0 | MEG_5400 | Drugs:betalactams:Penicillin_binding_protein:PBP2 | NA |
| contig00001 | 231621 | 232925 | PBP4B | 0/0 | 100.0 | 99.9 | MEG_5409 | Drugs:betalactams:Penicillin_binding_protein:PBP4B | NA |
| contig00001 | 62154 | 63122 | PMRF | 0/0 | 100.0 | 100.0 | MEG_5801 | Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF | NA |
| contig00046 | 11694 | 12350 | QNRS | 0/0 | 100.0 | 100.0 | MEG_6020 | Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS | NA |
| contig00027 | 21726 | 22595 | ROBA | 0/0 | 100.0 | 98.8 | MEG_6082 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA | NA |
| contig00016 | 33290 | 33612 | SOXS | 0/0 | 99.7 | 99.7 | MEG_6551 | Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS | NA |
| contig00046 | 23969 | 24784 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00046 | 20321 | 21566 | TEM | 0/0 | 98.3 | 99.4 | MEG_6875 | Drugs:betalactams:Class_A_betalactamases:TEM | NA |
| contig00072 | 2385 | 3659 | TETA | 0/0 | 100.0 | 100.0 | MEG_7024 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA | NA |
| contig00001 | 2055 | 3698 | YOGI | 0/0 | 100.0 | 100.0 | MEG_7842 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00080 | 8052 | 8912 | aac(3)-IId_1 | 0/0 | 100.0 | 99.9 | EU022314 | aac(3)-IId | Gentamicin, Tobramycin |
| contig00080 | 6639 | 7441 | aph(3’’)-Ib_2 | 0/0 | 99.9 | 100.0 | AF024602 | aph(3’’)-Ib | Streptomycin |
| contig00080 | 5803 | 6639 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00114 | 93 | 905 | blaNDM-1_1 | 0/0 | 100.0 | 100.0 | FN396876 | blaNDM-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam |
| contig00003 | 199899 | 200729 | blaOXA-356_1 | 0/0 | 100.0 | 100.0 | KF297585 | blaOXA-356 | |
| contig00094 | 129 | 971 | blaOXA-420_1 | 0/0 | 100.0 | 100.0 | AB983359 | blaOXA-420 | |
| contig00092 | 121 | 1005 | mph(E)_1 | 0/0 | 100.0 | 100.0 | DQ839391 | mph(E) | Erythromycin |
| contig00092 | 1061 | 2536 | msr(E)_1 | 0/0 | 100.0 | 100.0 | FR751518 | msr(E) | |
| contig00080 | 2375 | 3190 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00094 | 2244 | 3365 | tet(39)_1 | 0/0 | 100.0 | 99.9 | KT346360 | tet(39) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00080 | 8052 | 8912 | AAC(3)-IId | 0/0 | 100.0 | 99.9 | EU022314.1:0-861 | AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli | aminoglycoside |
| contig00080 | 6639 | 7442 | APH(3’’)-Ib | 0/0 | 100.0 | 99.9 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00080 | 5803 | 6639 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00114 | 909 | 1243 | determinant_of_bleomycin_resistance | 0/0 | 91.5 | 100.0 | KC503911.1:9883-10249 | A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. | glycopeptide |
| contig00092 | 121 | 1005 | mphE | 0/0 | 100.0 | 100.0 | DQ839391.1:13757-12872 | mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 | macrolide |
| contig00092 | 1061 | 2536 | msrE | 0/0 | 100.0 | 100.0 | EU294228.1:21241-22717 | MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. | lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline |
| contig00114 | 93 | 905 | NDM-1 | 0/0 | 100.0 | 100.0 | FN396876:3219-2406 | NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. | carbapenem, cephalosporin, cephamycin, penam |
| contig00003 | 199899 | 200729 | OXA-356 | 0/0 | 100.0 | 100.0 | KF297585:0-831 | OXA-356 is a beta-lactamase. From the Lahey list of OXA beta-lactamases. | cephalosporin, penam |
| contig00094 | 129 | 971 | OXA-420 | 0/0 | 100.0 | 100.0 | AB983359:2425-3268 | From the Lahey list of beta-lactamases. Not yet released. | cephalosporin, penam |
| contig00080 | 2375 | 3190 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00094 | 2178 | 3365 | tet(39) | 0/0 | 100.0 | 99.9 | AY743590:0-1188 | Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00080 | 8052 | 8912 | (AGly)aac3-IId | 0/0 | 100 | 99.9 | EU022314:1-861 | (AGly)aac3-IId | NA |
| contig00080 | 6639 | 7442 | (AGly)strA | 0/0 | 100 | 100.0 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00080 | 5803 | 6639 | (AGly)strB | 0/0 | 100 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00114 | 93 | 905 | (Bla)blaNDM-1 | 0/0 | 100 | 100.0 | JQ080305:1-813 | (Bla)blaNDM-1 | NA |
| contig00003 | 199899 | 200729 | (Bla)blaOXA-230 | 0/0 | 100 | 99.0 | JQ422054:101-931 | (Bla)blaOXA-230 | NA |
| contig00094 | 129 | 971 | (Bla)blaOXA-58 | 0/0 | 100 | 99.6 | AY665723:3301-4143 | (Bla)blaOXA-58 | NA |
| contig00092 | 121 | 1005 | (MLS)mph(E) | 0/0 | 100 | 99.9 | JF769133:8777-9661 | (MLS)mph(E) | NA |
| contig00092 | 1061 | 2536 | (MLS)msr(E) | 0/0 | 100 | 100.0 | JF769133:7246-8721 | (MLS)msr(E) | NA |
| contig00080 | 2375 | 3190 | (Sul)sul2 | 0/0 | 100 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00094 | 2178 | 3365 | (Tet)tet(39) | 0/0 | 100 | 99.9 | AY743590:749-1936 | (Tet)tet(39) | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00080 | 8052 | 8912 | aac(3)-IId | 0/0 | 100.0 | 100.0 | NG_047251.1 | aminoglycoside N-acetyltransferase AAC(3)-IId | GENTAMICIN |
| contig00080 | 6639 | 7466 | aph(3’’)-Ib | 0/0 | 100.0 | 99.9 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00080 | 5803 | 6639 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00114 | 93 | 905 | blaNDM-1 | 0/0 | 100.0 | 100.0 | NG_049326.1 | subclass B1 metallo-beta-lactamase NDM-1 | CARBAPENEM |
| contig00003 | 199899 | 200729 | blaOXA-356 | 0/0 | 100.0 | 100.0 | NG_049649.1 | OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-356 | CARBAPENEM |
| contig00094 | 129 | 971 | blaOXA-420 | 0/0 | 100.0 | 100.0 | NG_049708.1 | OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 | CARBAPENEM |
| contig00114 | 909 | 1243 | ble-MBL | 0/0 | 91.5 | 100.0 | NG_047559.1 | bleomycin binding protein Ble-MBL | BLEOMYCIN |
| contig00092 | 121 | 1005 | mph(E) | 0/0 | 100.0 | 100.0 | NG_064660.1 | Mph(E) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00092 | 1061 | 2536 | msr(E) | 0/0 | 100.0 | 100.0 | NG_048007.1 | ABC-F type ribosomal protection protein Msr(E) | MACROLIDE |
| contig00080 | 2375 | 3190 | sul2 | 0/0 | 100.0 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00094 | 2178 | 3365 | tet(39) | 0/0 | 100.0 | 99.9 | NG_048137.1 | tetracycline efflux MFS transporter Tet(39) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00080 | 8052 | 8912 | AAC3 | 0/0 | 100.0 | 100.0 | MEG_64 | Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 | NA |
| contig00080 | 6639 | 7466 | APH3-DPRIME | 0/0 | 100.0 | 99.9 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00080 | 5803 | 6639 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00114 | 909 | 1243 | BRP | 0/0 | 91.5 | 100.0 | MEG_1477 | Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP | NA |
| contig00092 | 121 | 1005 | MPHE | 0/0 | 100.0 | 100.0 | MEG_4044 | Drugs:MLS:Macrolide_phosphotransferases:MPHE | NA |
| contig00092 | 1061 | 2536 | MSRE | 0/0 | 100.0 | 100.0 | MEG_4075 | Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE | NA |
| contig00114 | 93 | 905 | NDM | 0/0 | 100.0 | 100.0 | MEG_4143 | Drugs:betalactams:Class_B_betalactamases:NDM | NA |
| contig00003 | 199864 | 200829 | OXA | 0/0 | 100.0 | 98.9 | MEG_5220 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00094 | 123 | 998 | OXA | 0/0 | 96.2 | 99.5 | MEG_5259 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00080 | 2375 | 3190 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00094 | 2178 | 3365 | TET39 | 0/0 | 100.0 | 99.9 | MEG_6987 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00035 | 4721 | 5254 | ant(2’’)-Ia_13 | 0/0 | 100 | 99.1 | DQ176450 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00024 | 9 | 1160 | blaADC-25_1 | 0/0 | 100 | 99.7 | EF016355 | blaADC-25 | |
| contig00006 | 209827 | 210651 | blaOXA-69_1 | 0/0 | 100 | 100.0 | AY859527 | blaOXA-69 | Amoxicillin, Ampicillin |
| contig00036 | 448 | 1263 | sul2_2 | 0/0 | 100 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00004 | 12051 | 13397 | abeM | 0/0 | 100 | 98.9 | AB204810:186-1533 | AbeM is an multidrug efflux pump found in Acinetobacter baumannii. | acridine_dye, fluoroquinolone, triclosan |
| contig00003 | 77408 | 77737 | abeS | 0/0 | 100 | 100.0 | CP001172.1:1249348-1249018 | AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. | aminocoumarin, macrolide |
| contig00025 | 28121 | 29410 | Acinetobacter_baumannii_AbaF | 0/0 | 100 | 97.9 | CP000521.1:1558523-1557233 | Expression of abaF in E. coli resulted in increased resistance to fosfomycin. | fosfomycin |
| contig00010 | 117010 | 118314 | Acinetobacter_baumannii_AbaQ | 0/0 | 100 | 100.0 | CP001182.2:2256889-2255584 | AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii | fluoroquinolone |
| contig00008 | 90140 | 91618 | Acinetobacter_baumannii_AmvA | 0/0 | 100 | 100.0 | FJ911554.1:176-1655 | AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. | acridine_dye, macrolide |
| contig00024 | 9 | 1160 | ADC-73 | 0/0 | 100 | 99.9 | KP881233.1:0-1152 | A class C ADC beta-lactamase and cephalosporinase found in Acinetobacter baumannii | cephalosporin |
| contig00014 | 12728 | 13918 | adeA | 0/0 | 100 | 97.7 | AF370885.1:3438-4629 | AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. | glycylcycline, tetracycline |
| contig00014 | 9621 | 12728 | adeB | 0/0 | 100 | 97.8 | AF370885.1:4628-7736 | AdeB is the multidrug transporter of the adeABC efflux system. | glycylcycline, tetracycline |
| contig00014 | 8147 | 9544 | adeC | 0/0 | 100 | 95.4 | CP013924.1:2063742-2065140 | AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels and is not essential for antibiotic resistance. | glycylcycline, tetracycline |
| contig00003 | 68464 | 71643 | adeF | 0/0 | 100 | 100.0 | CT025801.2:0-3180 | AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. | fluoroquinolone, tetracycline |
| contig00003 | 71650 | 72870 | adeG | 0/0 | 100 | 100.0 | CT025800.2:0-1221 | AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00003 | 67003 | 68454 | adeH | 0/0 | 100 | 100.0 | CT025802.2:0-1452 | AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00013 | 41683 | 42933 | adeI | 0/0 | 100 | 100.0 | CP001182.2:3283426-3284677 | AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00013 | 42946 | 46122 | adeJ | 0/0 | 100 | 99.6 | AY769962:2434-5611 | AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00013 | 46122 | 47576 | adeK | 0/0 | 100 | 98.7 | AY769962:5610-7065 | AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00003 | 73086 | 74099 | adeL | 0/0 | 100 | 99.4 | KR297239.1:1428-414 | AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. | fluoroquinolone, tetracycline |
| contig00008 | 35419 | 36072 | adeN | 0/0 | 100 | 98.0 | KF147862:0-654 | AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00014 | 14064 | 14807 | adeR | 0/0 | 100 | 100.0 | HM440348:0-744 | AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. | glycylcycline, tetracycline |
| contig00014 | 14839 | 15924 | adeS | 0/0 | 100 | 99.7 | HM440348:775-1861 | AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. | glycylcycline, tetracycline |
| contig00035 | 4721 | 5254 | ANT(2’’)-Ia | 0/0 | 100 | 98.9 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig00006 | 209827 | 210651 | OXA-69 | 0/0 | 100 | 100.0 | CU459141.1:2175316-2176141 | OXA-69 is a beta-lactamase found in A. baumannii | cephalosporin, penam |
| contig00036 | 448 | 1263 | sul2 | 0/0 | 100 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00035 | 4721 | 5254 | (AGly)aadB | 0/0 | 100 | 98.9 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig00021 | 23718 | 24506 | (AGly)ant(3’’)-IIa | 0/0 | 100 | 98.9 | NG_054648:101-889 | (AGly)ant(3’’)-IIa | NA |
| contig00010 | 129920 | 130939 | (Bla)BlaA1 | 0/0 | 100 | 100.0 | NC_010410:1803480-1804499 | (Bla)BlaA1 | NA |
| contig00019 | 57121 | 58395 | (Bla)BlaA2 | 0/0 | 100 | 100.0 | NC_010410:2507740-2509014 | (Bla)BlaA2 | NA |
| contig00024 | 9 | 1160 | (Bla)blaADC-73 | 0/0 | 100 | 99.9 | KP881233:1-1152 | (Bla)blaADC-73 | NA |
| contig00006 | 209827 | 210651 | (Bla)blaOXA-69 | 0/0 | 100 | 100.0 | AY750911:1-825 | (Bla)blaOXA-69 | NA |
| contig00006 | 30952 | 31647 | (Bla)Mbl | 0/0 | 100 | 100.0 | NC_010410:c1997136-1996441 | (Bla)Mbl | NA |
| contig00002 | 274643 | 275605 | (Bla)Zn-dependent_hydrolase | 0/0 | 100 | 100.0 | NC_010410:882015-882977 | (Bla)Zn-dependent_hydrolase | NA |
| contig00036 | 448 | 1263 | (Sul)sul2 | 0/0 | 100 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00035 | 4721 | 5254 | ant(2’’)-Ia | 0/0 | 100 | 99.1 | NG_052432.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig00021 | 23718 | 24506 | ant(3’’)-IIa | 0/0 | 100 | 100.0 | NG_054646.1 | aminoglycoside nucleotidyltransferase ANT(3’’)-IIa | SPECTINOMYCIN, STREPTOMYCIN |
| contig00024 | 9 | 1160 | blaADC-73 | 0/0 | 100 | 99.9 | NG_048678.1 | class C extended-spectrum beta-lactamase ADC-73 | CEPHALOSPORIN |
| contig00006 | 209827 | 210651 | blaOXA-69 | 0/0 | 100 | 100.0 | NG_049809.1 | OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69 | CARBAPENEM |
| contig00036 | 448 | 1263 | sul2 | 0/0 | 100 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00025 | 28121 | 29410 | ABAF | 0/0 | 100.0 | 97.9 | MEG_369 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF | NA |
| contig00010 | 117010 | 118314 | ABAQ | 0/0 | 100.0 | 100.0 | MEG_370 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ | NA |
| contig00004 | 12051 | 13397 | ABEM | 0/0 | 100.0 | 98.9 | MEG_372 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM | NA |
| contig00003 | 77408 | 77737 | ABES | 0/0 | 100.0 | 100.0 | MEG_379 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES | NA |
| contig00024 | 9 | 1160 | ADC | 0/0 | 100.0 | 99.9 | MEG_666 | Drugs:betalactams:Class_C_betalactamases:ADC | NA |
| contig00014 | 12728 | 13918 | ADEA | 0/0 | 100.0 | 97.7 | MEG_677 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA | NA |
| contig00014 | 9621 | 12728 | ADEB | 0/0 | 100.0 | 97.8 | MEG_678 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB | NA |
| contig00014 | 8147 | 9544 | ADEC | 0/0 | 100.0 | 95.4 | MEG_679 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEC | NA |
| contig00003 | 71650 | 72870 | ADEF | 0/0 | 100.0 | 100.0 | MEG_683 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEF | NA |
| contig00003 | 68464 | 71643 | ADEG | 0/0 | 100.0 | 100.0 | MEG_684 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG | NA |
| contig00003 | 67003 | 68454 | ADEH | 0/0 | 100.0 | 100.0 | MEG_685 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH | NA |
| contig00013 | 41683 | 42933 | ADEI | 0/0 | 100.0 | 100.0 | MEG_686 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI | NA |
| contig00013 | 42946 | 46122 | ADEJ | 0/0 | 100.0 | 99.6 | MEG_692 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ | NA |
| contig00013 | 46122 | 47576 | ADEK | 0/0 | 100.0 | 99.0 | MEG_696 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK | NA |
| contig00003 | 73086 | 74099 | ADEL | 0/0 | 100.0 | 99.5 | MEG_699 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL | NA |
| contig00008 | 35419 | 36072 | ADEN | 0/0 | 100.0 | 100.0 | MEG_701 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN | NA |
| contig00014 | 14064 | 14807 | ADER | 0/0 | 100.0 | 100.0 | MEG_703 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER | NA |
| contig00014 | 14839 | 15924 | ADES | 0/0 | 100.0 | 99.7 | MEG_704 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES | NA |
| contig00001 | 406388 | 407104 | ADET2 | 0/0 | 100.0 | 98.9 | MEG_706 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 | NA |
| contig00008 | 90140 | 91618 | AMVA | 0/0 | 100.0 | 100.0 | MEG_733 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA | NA |
| contig00021 | 23718 | 24506 | ANT3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_913 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00010 | 129920 | 130939 | BLAA | 0/0 | 100.0 | 100.0 | MEG_1246 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00019 | 57121 | 58395 | BLAA | 0/0 | 100.0 | 100.0 | MEG_1247 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00005 | 71704 | 72693 | MEXT | 0/0 | 100.0 | 98.8 | MEG_3934 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT | NA |
| contig00006 | 209782 | 210733 | OXA | 3/3 | 98.9 | 97.5 | MEG_5236 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00036 | 448 | 1263 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00154 | 3439 | 4240 | aadA2_1 | 0/0 | 97.9 | 99.9 | NC_010870 | aadA2 | Streptomycin |
| contig00146 | 1510 | 2312 | aph(3’’)-Ib_2 | 0/0 | 99.9 | 100.0 | AF024602 | aph(3’’)-Ib | Streptomycin |
| contig00146 | 674 | 1510 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00040 | 19695 | 20840 | blaACT-6_1 | 0/0 | 100.0 | 91.0 | FJ237366 | blaACT-6 | |
| contig00099 | 5508 | 6383 | blaCTX-M-3_1 | 0/0 | 100.0 | 100.0 | Y10278 | blaCTX-M-3 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig00099 | 3866 | 4726 | blaTEM-1B_1 | 0/0 | 100.0 | 100.0 | AY458016 | blaTEM-1B | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin |
| contig00154 | 4638 | 5135 | dfrA12_8 | 0/0 | 100.0 | 100.0 | AM040708 | dfrA12 | Trimethoprim |
| contig00058 | 20141 | 20566 | fosA_1 | 0/0 | 100.0 | 95.1 | M85195 | fosA | Fosfomycin |
| contig00099 | 13087 | 13743 | qnrS1_1 | 0/0 | 100.0 | 100.0 | AB187515 | qnrS1 | Ciprofloxacin |
| contig00154 | 2095 | 2961 | sul1_5 | 0/0 | 100.0 | 99.9 | EU780013 | sul1 | Sulfamethoxazole |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00154 | 3439 | 4218 | aadA2 | 0/0 | 100.0 | 99.9 | AF156486:5012-5792 | aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp. | aminoglycoside |
| contig00040 | 19695 | 20840 | ACT-6 | 0/0 | 100.0 | 91.0 | FJ237366:40-1186 | ACT-6 is a beta-lactamase found in Klebsiella pneumoniae | carbapenem, cephalosporin, cephamycin, penam |
| contig00146 | 1510 | 2313 | APH(3’’)-Ib | 0/0 | 100.0 | 99.9 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00146 | 674 | 1510 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00099 | 5508 | 6383 | CTX-M-3 | 0/0 | 100.0 | 100.0 | Y10278:0-876 | CTX-M-3 is a beta-lactamase found in Citrobacter freundii | cephalosporin |
| contig00154 | 4638 | 5135 | dfrA12 | 0/0 | 100.0 | 100.0 | GU585907.1:22103-21605 | dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae | diaminopyrimidine |
| contig00074 | 14977 | 16170 | Enterobacter_cloacae_acrA | 0/0 | 100.0 | 95.2 | DQ679966:299-1493 | AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae. | cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00058 | 20141 | 20566 | FosA2 | 2/4 | 99.5 | 92.3 | EU487198:216-642 | An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. | fosfomycin |
| contig00099 | 13087 | 13743 | QnrS1 | 0/0 | 100.0 | 100.0 | DQ485529.1:0-657 | QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri | fluoroquinolone |
| contig00139 | 4345 | 4708 | ramA | 0/0 | 97.1 | 90.9 | JQ727668:0-375 | RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. | carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan |
| contig00154 | 2095 | 2934 | sul1 | 0/0 | 100.0 | 100.0 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig00099 | 3866 | 4726 | TEM-1 | 0/0 | 100.0 | 99.9 | AL513383:161910-162771 | TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. | cephalosporin, monobactam, penam, penem |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00154 | 3439 | 4218 | (AGly)aadA2 | 0/0 | 100.0 | 99.9 | X68227:66-945 | (AGly)aadA2 | NA |
| contig00146 | 1510 | 2313 | (AGly)strA | 0/0 | 100.0 | 100.0 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00146 | 674 | 1510 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00040 | 19695 | 20840 | (Bla)blaACT-6 | 0/0 | 100.0 | 91.0 | FJ237366:41-1186 | (Bla)blaACT-6 | NA |
| contig00099 | 5508 | 6383 | (Bla)blaCTX-M-3 | 0/0 | 100.0 | 100.0 | Y10278:1-876 | (Bla)blaCTX-M-3 | NA |
| contig00099 | 3866 | 4726 | (Bla)blaTEM-105 | 0/0 | 100.0 | 99.9 | AF516720:215-1075 | (Bla)blaTEM-105 | NA |
| contig00058 | 20141 | 20566 | (Fcyn)FosA2 | 2/4 | 99.5 | 92.3 | EU487198:217-642 | (Fcyn)FosA2 | NA |
| contig00099 | 13087 | 13743 | (Flq)qnr-S1 | 0/0 | 100.0 | 100.0 | AB187515:9737-10393 | (Flq)qnr-S1 | NA |
| contig00154 | 2095 | 2934 | (Sul)sul1 | 0/0 | 100.0 | 100.0 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig00154 | 4638 | 5135 | (Tmt)dfrA12 | 0/0 | 100.0 | 100.0 | Z21672:310-807 | (Tmt)dfrA12 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00154 | 3439 | 4230 | aadA2 | 0/0 | 100 | 100.0 | NG_047343.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2 | STREPTOMYCIN |
| contig00146 | 1510 | 2337 | aph(3’’)-Ib | 0/0 | 100 | 99.9 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00146 | 674 | 1510 | aph(6)-Id | 0/0 | 100 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00040 | 19695 | 20840 | blaACT-53 | 0/0 | 100 | 100.0 | NG_055522.1 | cephalosporin-hydrolyzing class C beta-lactamase ACT-53 | CEPHALOSPORIN |
| contig00099 | 5508 | 6383 | blaCTX-M-3 | 0/0 | 100 | 100.0 | NG_048979.1 | class A extended-spectrum beta-lactamase CTX-M-3 | CEPHALOSPORIN |
| contig00099 | 3866 | 4726 | blaTEM-1 | 0/0 | 100 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00154 | 4638 | 5135 | dfrA12 | 0/0 | 100 | 100.0 | NG_047689.1 | trimethoprim-resistant dihydrofolate reductase DfrA12 | TRIMETHOPRIM |
| contig00058 | 20141 | 20566 | fosA | 0/0 | 100 | 95.1 | NG_050405.1 | fosfomycin resistance glutathione transferase FosA | FOSFOMYCIN |
| contig00099 | 13087 | 13743 | qnrS1 | 0/0 | 100 | 100.0 | NG_050543.1 | quinolone resistance pentapeptide repeat protein QnrS1 | QUINOLONE |
| contig00154 | 2095 | 2934 | sul1 | 0/0 | 100 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00074 | 14977 | 16170 | ACRB | 0/0 | 100.0 | 95.2 | MEG_402 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB | NA |
| contig00040 | 19695 | 20840 | ACT | 0/0 | 100.0 | 100.0 | MEG_441 | Drugs:betalactams:Class_C_betalactamases:ACT | NA |
| contig00154 | 3439 | 4240 | ANT3-DPRIME | 0/0 | 97.9 | 99.9 | MEG_975 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00146 | 1510 | 2337 | APH3-DPRIME | 0/0 | 100.0 | 99.9 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00146 | 674 | 1510 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00099 | 5137 | 6622 | CTX | 0/0 | 100.0 | 99.8 | MEG_2421 | Drugs:betalactams:Class_A_betalactamases:CTX | NA |
| contig00154 | 4638 | 5135 | DFRA | 0/0 | 100.0 | 100.0 | MEG_2551 | Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA | NA |
| contig00058 | 19987 | 20566 | FOSA | 2/4 | 99.3 | 92.8 | MEG_2990 | Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA | NA |
| contig00099 | 13087 | 13743 | QNRS | 0/0 | 100.0 | 100.0 | MEG_6020 | Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS | NA |
| contig00139 | 4345 | 4708 | RAMA | 0/0 | 97.1 | 90.9 | MEG_6044 | Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA | NA |
| contig00154 | 1968 | 2935 | SULI | 0/0 | 100.0 | 100.0 | MEG_6615 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI | NA |
| contig00099 | 3499 | 4744 | TEM | 0/0 | 98.3 | 99.4 | MEG_6875 | Drugs:betalactams:Class_A_betalactamases:TEM | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00032 | 34599 | 35750 | blaADC-25_1 | 0/0 | 100.0 | 97.1 | EF016355 | blaADC-25 | |
| contig00061 | 92 | 904 | blaNDM-1_1 | 0/0 | 100.0 | 100.0 | FN396876 | blaNDM-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam |
| contig00018 | 70816 | 71640 | blaOXA-98_1 | 0/0 | 100.0 | 99.9 | EU255288 | blaOXA-98 | |
| contig00033 | 19356 | 20569 | floR_2 | 0/0 | 99.9 | 98.3 | AF118107 | floR | Chloramphenicol, Florfenicol |
| contig00033 | 29463 | 30347 | mph(E)_1 | 0/0 | 100.0 | 100.0 | DQ839391 | mph(E) | Erythromycin |
| contig00033 | 27932 | 29407 | msr(E)_1 | 0/0 | 100.0 | 100.0 | FR751518 | msr(E) | |
| contig00014 | 89308 | 90123 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00033 | 22089 | 23210 | tet(39)_1 | 0/0 | 100.0 | 100.0 | KT346360 | tet(39) | Doxycycline, Tetracycline |
| contig00014 | 87488 | 88693 | tet(B)_1 | 0/0 | 100.0 | 100.0 | AP000342 | tet(B) | Doxycycline, Tetracycline, Minocycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00008 | 23968 | 25314 | abeM | 0/0 | 100.0 | 100.0 | AB204810:186-1533 | AbeM is an multidrug efflux pump found in Acinetobacter baumannii. | acridine_dye, fluoroquinolone, triclosan |
| contig00002 | 42631 | 42960 | abeS | 0/0 | 100.0 | 97.9 | CP001172.1:1249348-1249018 | AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. | aminocoumarin, macrolide |
| contig00005 | 10124 | 11413 | Acinetobacter_baumannii_AbaF | 0/0 | 100.0 | 96.8 | CP000521.1:1558523-1557233 | Expression of abaF in E. coli resulted in increased resistance to fosfomycin. | fosfomycin |
| contig00006 | 91623 | 92927 | Acinetobacter_baumannii_AbaQ | 0/0 | 100.0 | 95.6 | CP001182.2:2256889-2255584 | AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii | fluoroquinolone |
| contig00022 | 42414 | 43892 | Acinetobacter_baumannii_AmvA | 0/0 | 100.0 | 97.9 | FJ911554.1:176-1655 | AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. | acridine_dye, macrolide |
| contig00032 | 34599 | 35750 | ADC-2 | 0/0 | 100.0 | 99.7 | AY177427.1:1141-2293 | ADC-2 is a beta-lactamase found in Oligella urethralis. | cephalosporin |
| contig00047 | 8886 | 10076 | adeA | 0/0 | 100.0 | 97.7 | AF370885.1:3438-4629 | AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. | glycylcycline, tetracycline |
| contig00047 | 10076 | 13183 | adeB | 0/0 | 100.0 | 98.1 | AF370885.1:4628-7736 | AdeB is the multidrug transporter of the adeABC efflux system. | glycylcycline, tetracycline |
| contig00002 | 33687 | 36866 | adeF | 0/0 | 100.0 | 97.7 | CT025801.2:0-3180 | AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. | fluoroquinolone, tetracycline |
| contig00002 | 36873 | 38093 | adeG | 0/0 | 100.0 | 98.4 | CT025800.2:0-1221 | AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00002 | 32226 | 33677 | adeH | 0/0 | 100.0 | 98.5 | CT025802.2:0-1452 | AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00003 | 39967 | 41217 | adeI | 0/0 | 100.0 | 99.7 | CP001182.2:3283426-3284677 | AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00003 | 41230 | 44406 | adeJ | 0/0 | 100.0 | 99.6 | AY769962:2434-5611 | AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00003 | 44406 | 45860 | adeK | 0/0 | 100.0 | 98.8 | AY769962:5610-7065 | AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00002 | 38309 | 39322 | adeL | 0/0 | 100.0 | 99.7 | KR297239.1:1428-414 | AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. | fluoroquinolone, tetracycline |
| contig00031 | 26224 | 26877 | adeN | 0/0 | 100.0 | 98.5 | KF147862:0-654 | AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00047 | 7997 | 8740 | adeR | 0/0 | 100.0 | 98.1 | HM440348:0-744 | AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. | glycylcycline, tetracycline |
| contig00047 | 6901 | 7965 | adeS | 0/0 | 98.1 | 95.8 | HM440348:775-1861 | AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. | glycylcycline, tetracycline |
| contig00061 | 908 | 1273 | determinant_of_bleomycin_resistance | 0/0 | 100.0 | 100.0 | KC503911.1:9883-10249 | A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. | glycopeptide |
| contig00033 | 19356 | 20570 | floR | 0/0 | 100.0 | 99.9 | AF231986:3307-4522 | floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae | phenicol |
| contig00033 | 29463 | 30347 | mphE | 0/0 | 100.0 | 100.0 | DQ839391.1:13757-12872 | mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 | macrolide |
| contig00033 | 27932 | 29407 | msrE | 0/0 | 100.0 | 100.0 | EU294228.1:21241-22717 | MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. | lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline |
| contig00061 | 92 | 904 | NDM-1 | 0/0 | 100.0 | 100.0 | FN396876:3219-2406 | NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. | carbapenem, cephalosporin, cephamycin, penam |
| contig00018 | 70816 | 71640 | OXA-98 | 0/0 | 100.0 | 99.9 | AM279652:0-825 | OXA-98 is a beta-lactamase found in A. baumannii | cephalosporin, penam |
| contig00014 | 89308 | 90123 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00033 | 22089 | 23276 | tet(39) | 0/0 | 100.0 | 100.0 | AY743590:0-1188 | Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. | tetracycline |
| contig00014 | 87488 | 88693 | tet(B) | 0/0 | 100.0 | 99.8 | AB089595:0-1206 | Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00007 | 119028 | 119816 | (AGly)ant(3’’)-IIa | 0/0 | 100.0 | 100.0 | NG_054648:101-889 | (AGly)ant(3’’)-IIa | NA |
| contig00006 | 104506 | 105523 | (Bla)BlaA1 | 0/0 | 99.8 | 90.8 | NC_010410:1803480-1804499 | (Bla)BlaA1 | NA |
| contig00020 | 19863 | 21131 | (Bla)BlaA2 | 0/0 | 99.5 | 97.4 | NC_010410:2507740-2509014 | (Bla)BlaA2 | NA |
| contig00032 | 34599 | 35750 | (Bla)blaADC-2 | 0/0 | 100.0 | 99.7 | NG_048644:101-1252 | (Bla)blaADC-2 | NA |
| contig00061 | 92 | 904 | (Bla)blaNDM-1 | 0/0 | 100.0 | 100.0 | JQ080305:1-813 | (Bla)blaNDM-1 | NA |
| contig00018 | 70816 | 71640 | (Bla)blaOXA-98 | 0/0 | 100.0 | 99.9 | AM279652:1-825 | (Bla)blaOXA-98 | NA |
| contig00021 | 33771 | 34466 | (Bla)Mbl | 0/0 | 100.0 | 98.0 | NC_010410:c1997136-1996441 | (Bla)Mbl | NA |
| contig00019 | 50318 | 51280 | (Bla)Zn-dependent_hydrolase | 0/0 | 100.0 | 98.7 | NC_010410:882015-882977 | (Bla)Zn-dependent_hydrolase | NA |
| contig00033 | 29463 | 30347 | (MLS)mph(E) | 0/0 | 100.0 | 99.9 | JF769133:8777-9661 | (MLS)mph(E) | NA |
| contig00033 | 27932 | 29407 | (MLS)msr(E) | 0/0 | 100.0 | 100.0 | JF769133:7246-8721 | (MLS)msr(E) | NA |
| contig00033 | 19356 | 20570 | (Phe)floR | 0/0 | 100.0 | 99.8 | AKLJ01000508:383-1597 | (Phe)floR | NA |
| contig00014 | 89308 | 90123 | (Sul)sul2 | 0/0 | 100.0 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00033 | 22089 | 23276 | (Tet)tet(39) | 0/0 | 100.0 | 100.0 | AY743590:749-1936 | (Tet)tet(39) | NA |
| contig00014 | 87488 | 88693 | (Tet)tetB | 0/0 | 100.0 | 99.8 | AB089594:1-1206 | (Tet)tetB | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00007 | 119028 | 119816 | ant(3’’)-IIa | 0/0 | 100 | 100.0 | NG_054648.1 | aminoglycoside nucleotidyltransferase ANT(3’’)-IIa | SPECTINOMYCIN, STREPTOMYCIN |
| contig00032 | 34599 | 35750 | blaADC-158 | 0/0 | 100 | 100.0 | NG_055786.1 | class C beta-lactamase ADC-158 | CEPHALOSPORIN |
| contig00061 | 92 | 904 | blaNDM-1 | 0/0 | 100 | 100.0 | NG_049326.1 | subclass B1 metallo-beta-lactamase NDM-1 | CARBAPENEM |
| contig00018 | 70816 | 71640 | blaOXA-694 | 0/0 | 100 | 99.9 | NG_062316.1 | OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-694 | BETA-LACTAM |
| contig00061 | 908 | 1273 | ble-MBL | 0/0 | 100 | 100.0 | NG_047559.1 | bleomycin binding protein Ble-MBL | BLEOMYCIN |
| contig00033 | 19356 | 20570 | floR | 0/0 | 100 | 100.0 | NG_047869.1 | chloramphenicol/florfenicol efflux MFS transporter FloR | CHLORAMPHENICOL, FLORFENICOL |
| contig00033 | 29463 | 30347 | mph(E) | 0/0 | 100 | 100.0 | NG_064660.1 | Mph(E) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00033 | 27932 | 29407 | msr(E) | 0/0 | 100 | 100.0 | NG_048007.1 | ABC-F type ribosomal protection protein Msr(E) | MACROLIDE |
| contig00014 | 89308 | 90123 | sul2 | 0/0 | 100 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00033 | 22089 | 23276 | tet(39) | 0/0 | 100 | 100.0 | NG_048137.1 | tetracycline efflux MFS transporter Tet(39) | TETRACYCLINE |
| contig00014 | 87488 | 88693 | tet(B) | 0/0 | 100 | 100.0 | NG_048161.1 | tetracycline efflux MFS transporter Tet(B) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00005 | 10124 | 11413 | ABAF | 0/0 | 100.0 | 96.8 | MEG_369 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF | NA |
| contig00006 | 91623 | 92927 | ABAQ | 0/0 | 100.0 | 95.6 | MEG_370 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ | NA |
| contig00008 | 23968 | 25314 | ABEM | 0/0 | 100.0 | 100.0 | MEG_373 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM | NA |
| contig00002 | 42631 | 42960 | ABES | 0/0 | 100.0 | 99.4 | MEG_378 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES | NA |
| contig00032 | 34599 | 35750 | ADC | 0/0 | 100.0 | 100.0 | MEG_575 | Drugs:betalactams:Class_C_betalactamases:ADC | NA |
| contig00047 | 8886 | 10076 | ADEA | 0/0 | 100.0 | 97.7 | MEG_677 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA | NA |
| contig00047 | 10076 | 13183 | ADEB | 0/0 | 100.0 | 98.1 | MEG_678 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB | NA |
| contig00002 | 33687 | 36866 | ADEG | 0/0 | 100.0 | 97.7 | MEG_684 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG | NA |
| contig00002 | 32226 | 33677 | ADEH | 0/0 | 100.0 | 98.5 | MEG_685 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH | NA |
| contig00003 | 39967 | 41217 | ADEI | 0/0 | 100.0 | 99.9 | MEG_689 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI | NA |
| contig00003 | 41230 | 44406 | ADEJ | 0/0 | 100.0 | 99.6 | MEG_692 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ | NA |
| contig00003 | 44406 | 45860 | ADEK | 0/0 | 100.0 | 99.1 | MEG_698 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK | NA |
| contig00002 | 38309 | 39322 | ADEL | 0/0 | 100.0 | 99.7 | MEG_700 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL | NA |
| contig00031 | 26224 | 26877 | ADEN | 0/0 | 100.0 | 98.5 | MEG_702 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN | NA |
| contig00047 | 7997 | 8740 | ADER | 0/0 | 100.0 | 98.1 | MEG_703 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER | NA |
| contig00047 | 6901 | 7965 | ADES | 0/0 | 98.1 | 95.8 | MEG_704 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES | NA |
| contig00047 | 5773 | 6687 | ADET1 | 0/0 | 100.0 | 96.7 | MEG_705 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET1 | NA |
| contig00013 | 46951 | 47667 | ADET2 | 0/0 | 100.0 | 98.9 | MEG_706 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 | NA |
| contig00022 | 42414 | 43892 | AMVA | 0/0 | 100.0 | 97.9 | MEG_733 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA | NA |
| contig00007 | 119028 | 119816 | ANT3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_899 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00006 | 104506 | 105523 | BLAA | 0/0 | 99.8 | 90.8 | MEG_1246 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00020 | 19863 | 21131 | BLAA | 0/0 | 99.5 | 97.4 | MEG_1247 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00061 | 908 | 1273 | BRP | 0/0 | 100.0 | 100.0 | MEG_1477 | Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP | NA |
| contig00033 | 19356 | 20570 | FLOR | 0/0 | 100.0 | 100.0 | MEG_2923 | Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR | NA |
| contig00002 | 36873 | 38093 | MEXE | 1/3 | 100.0 | 99.1 | MEG_3910 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MEXE | NA |
| contig00039 | 1751 | 2740 | MEXT | 0/0 | 100.0 | 98.7 | MEG_3934 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT | NA |
| contig00033 | 29463 | 30347 | MPHE | 0/0 | 100.0 | 100.0 | MEG_4044 | Drugs:MLS:Macrolide_phosphotransferases:MPHE | NA |
| contig00033 | 27932 | 29407 | MSRE | 0/0 | 100.0 | 100.0 | MEG_4075 | Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE | NA |
| contig00061 | 92 | 904 | NDM | 0/0 | 100.0 | 100.0 | MEG_4143 | Drugs:betalactams:Class_B_betalactamases:NDM | NA |
| contig00018 | 70771 | 71722 | OXA | 3/3 | 99.0 | 98.5 | MEG_5236 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00014 | 89308 | 90123 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00033 | 22089 | 23276 | TET39 | 0/0 | 100.0 | 100.0 | MEG_6987 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 | NA |
| contig00014 | 87488 | 88693 | TETB | 0/0 | 100.0 | 100.0 | MEG_7042 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00037 | 4721 | 5254 | ant(2’’)-Ia_13 | 0/0 | 100 | 99.1 | DQ176450 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00002 | 9 | 1160 | blaADC-25_1 | 0/0 | 100 | 99.8 | EF016355 | blaADC-25 | |
| contig00006 | 209855 | 210679 | blaOXA-69_1 | 0/0 | 100 | 100.0 | AY859527 | blaOXA-69 | Amoxicillin, Ampicillin |
| contig00038 | 448 | 1263 | sul2_2 | 0/0 | 100 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00007 | 12051 | 13397 | abeM | 0/0 | 100 | 98.9 | AB204810:186-1533 | AbeM is an multidrug efflux pump found in Acinetobacter baumannii. | acridine_dye, fluoroquinolone, triclosan |
| contig00009 | 77408 | 77737 | abeS | 0/0 | 100 | 100.0 | CP001172.1:1249348-1249018 | AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. | aminocoumarin, macrolide |
| contig00004 | 134203 | 135492 | Acinetobacter_baumannii_AbaF | 0/0 | 100 | 97.9 | CP000521.1:1558523-1557233 | Expression of abaF in E. coli resulted in increased resistance to fosfomycin. | fosfomycin |
| contig00011 | 116965 | 118269 | Acinetobacter_baumannii_AbaQ | 0/0 | 100 | 100.0 | CP001182.2:2256889-2255584 | AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii | fluoroquinolone |
| contig00012 | 90155 | 91633 | Acinetobacter_baumannii_AmvA | 0/0 | 100 | 100.0 | FJ911554.1:176-1655 | AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. | acridine_dye, macrolide |
| contig00002 | 9 | 1160 | ADC-73 | 0/0 | 100 | 100.0 | KP881233.1:0-1152 | A class C ADC beta-lactamase and cephalosporinase found in Acinetobacter baumannii | cephalosporin |
| contig00016 | 12626 | 13816 | adeA | 0/0 | 100 | 97.7 | AF370885.1:3438-4629 | AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. | glycylcycline, tetracycline |
| contig00016 | 9519 | 12626 | adeB | 0/0 | 100 | 97.8 | AF370885.1:4628-7736 | AdeB is the multidrug transporter of the adeABC efflux system. | glycylcycline, tetracycline |
| contig00016 | 8045 | 9442 | adeC | 0/0 | 100 | 95.4 | CP013924.1:2063742-2065140 | AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels and is not essential for antibiotic resistance. | glycylcycline, tetracycline |
| contig00009 | 68464 | 71643 | adeF | 0/0 | 100 | 100.0 | CT025801.2:0-3180 | AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. | fluoroquinolone, tetracycline |
| contig00009 | 71650 | 72870 | adeG | 0/0 | 100 | 100.0 | CT025800.2:0-1221 | AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00009 | 67003 | 68454 | adeH | 0/0 | 100 | 100.0 | CT025802.2:0-1452 | AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. | fluoroquinolone, tetracycline |
| contig00003 | 41699 | 42949 | adeI | 0/0 | 100 | 100.0 | CP001182.2:3283426-3284677 | AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00003 | 42962 | 46138 | adeJ | 0/0 | 100 | 99.6 | AY769962:2434-5611 | AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00003 | 46138 | 47592 | adeK | 0/0 | 100 | 98.7 | AY769962:5610-7065 | AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00009 | 73086 | 74099 | adeL | 0/0 | 100 | 99.4 | KR297239.1:1428-414 | AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. | fluoroquinolone, tetracycline |
| contig00012 | 35446 | 36099 | adeN | 0/0 | 100 | 98.0 | KF147862:0-654 | AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. | carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline |
| contig00016 | 13962 | 14705 | adeR | 0/0 | 100 | 100.0 | HM440348:0-744 | AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. | glycylcycline, tetracycline |
| contig00016 | 14737 | 15822 | adeS | 0/0 | 100 | 99.7 | HM440348:775-1861 | AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. | glycylcycline, tetracycline |
| contig00037 | 4721 | 5254 | ANT(2’’)-Ia | 0/0 | 100 | 98.9 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig00006 | 209855 | 210679 | OXA-69 | 0/0 | 100 | 100.0 | CU459141.1:2175316-2176141 | OXA-69 is a beta-lactamase found in A. baumannii | cephalosporin, penam |
| contig00038 | 448 | 1263 | sul2 | 0/0 | 100 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00037 | 4721 | 5254 | (AGly)aadB | 0/0 | 100 | 98.9 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig00021 | 23924 | 24712 | (AGly)ant(3’’)-IIa | 0/0 | 100 | 98.9 | NG_054648:101-889 | (AGly)ant(3’’)-IIa | NA |
| contig00011 | 129875 | 130894 | (Bla)BlaA1 | 0/0 | 100 | 100.0 | NC_010410:1803480-1804499 | (Bla)BlaA1 | NA |
| contig00004 | 52665 | 53939 | (Bla)BlaA2 | 0/0 | 100 | 100.0 | NC_010410:2507740-2509014 | (Bla)BlaA2 | NA |
| contig00002 | 9 | 1160 | (Bla)blaADC-73 | 0/0 | 100 | 100.0 | KP881233:1-1152 | (Bla)blaADC-73 | NA |
| contig00006 | 209855 | 210679 | (Bla)blaOXA-69 | 0/0 | 100 | 100.0 | AY750911:1-825 | (Bla)blaOXA-69 | NA |
| contig00006 | 30980 | 31675 | (Bla)Mbl | 0/0 | 100 | 100.0 | NC_010410:c1997136-1996441 | (Bla)Mbl | NA |
| contig00002 | 315355 | 316317 | (Bla)Zn-dependent_hydrolase | 0/0 | 100 | 100.0 | NC_010410:882015-882977 | (Bla)Zn-dependent_hydrolase | NA |
| contig00038 | 448 | 1263 | (Sul)sul2 | 0/0 | 100 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00037 | 4721 | 5254 | ant(2’’)-Ia | 0/0 | 100 | 99.1 | NG_052432.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig00021 | 23924 | 24712 | ant(3’’)-IIa | 0/0 | 100 | 100.0 | NG_054646.1 | aminoglycoside nucleotidyltransferase ANT(3’’)-IIa | SPECTINOMYCIN, STREPTOMYCIN |
| contig00002 | 9 | 1160 | blaADC-73 | 0/0 | 100 | 100.0 | NG_048678.1 | class C extended-spectrum beta-lactamase ADC-73 | CEPHALOSPORIN |
| contig00006 | 209855 | 210679 | blaOXA-69 | 0/0 | 100 | 100.0 | NG_049809.1 | OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69 | CARBAPENEM |
| contig00038 | 448 | 1263 | sul2 | 0/0 | 100 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00004 | 134203 | 135492 | ABAF | 0/0 | 100.0 | 97.9 | MEG_369 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF | NA |
| contig00011 | 116965 | 118269 | ABAQ | 0/0 | 100.0 | 100.0 | MEG_370 | Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ | NA |
| contig00007 | 12051 | 13397 | ABEM | 0/0 | 100.0 | 98.9 | MEG_372 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM | NA |
| contig00009 | 77408 | 77737 | ABES | 0/0 | 100.0 | 100.0 | MEG_379 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES | NA |
| contig00002 | 9 | 1160 | ADC | 0/0 | 100.0 | 100.0 | MEG_666 | Drugs:betalactams:Class_C_betalactamases:ADC | NA |
| contig00016 | 12626 | 13816 | ADEA | 0/0 | 100.0 | 97.7 | MEG_677 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA | NA |
| contig00016 | 9519 | 12626 | ADEB | 0/0 | 100.0 | 97.8 | MEG_678 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB | NA |
| contig00016 | 8045 | 9442 | ADEC | 0/0 | 100.0 | 95.4 | MEG_679 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEC | NA |
| contig00009 | 71650 | 72870 | ADEF | 0/0 | 100.0 | 100.0 | MEG_683 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEF | NA |
| contig00009 | 68464 | 71643 | ADEG | 0/0 | 100.0 | 100.0 | MEG_684 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG | NA |
| contig00009 | 67003 | 68454 | ADEH | 0/0 | 100.0 | 100.0 | MEG_685 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH | NA |
| contig00003 | 41699 | 42949 | ADEI | 0/0 | 100.0 | 100.0 | MEG_686 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI | NA |
| contig00003 | 42962 | 46138 | ADEJ | 0/0 | 100.0 | 99.6 | MEG_692 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ | NA |
| contig00003 | 46138 | 47592 | ADEK | 0/0 | 100.0 | 99.0 | MEG_696 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK | NA |
| contig00009 | 73086 | 74099 | ADEL | 0/0 | 100.0 | 99.5 | MEG_699 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL | NA |
| contig00012 | 35446 | 36099 | ADEN | 0/0 | 100.0 | 100.0 | MEG_701 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN | NA |
| contig00016 | 13962 | 14705 | ADER | 0/0 | 100.0 | 100.0 | MEG_703 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER | NA |
| contig00016 | 14737 | 15822 | ADES | 0/0 | 100.0 | 99.7 | MEG_704 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES | NA |
| contig00015 | 48180 | 48896 | ADET2 | 0/0 | 100.0 | 98.9 | MEG_706 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 | NA |
| contig00012 | 90155 | 91633 | AMVA | 0/0 | 100.0 | 100.0 | MEG_733 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA | NA |
| contig00021 | 23924 | 24712 | ANT3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_913 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00004 | 52665 | 53939 | BLAA | 0/0 | 100.0 | 100.0 | MEG_1247 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00011 | 129875 | 130894 | BLAA | 0/0 | 100.0 | 100.0 | MEG_1246 | Drugs:betalactams:Class_A_betalactamases:BLAA | NA |
| contig00024 | 38317 | 39306 | MEXT | 0/0 | 100.0 | 98.8 | MEG_3934 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT | NA |
| contig00006 | 209810 | 210761 | OXA | 3/3 | 98.9 | 97.5 | MEG_5236 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00038 | 448 | 1263 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00250 | 1696 | 2556 | aac(3)-IIa_1 | 0/0 | 100.0 | 99.8 | X51534 | aac(3)-IIa | Gentamicin, Tobramycin |
| contig00261 | 1539 | 2138 | aac(6’)-Ib-cr_1 | 0/0 | 100.0 | 100.0 | DQ303918 | aac(6’)-Ib-cr | Ciprofloxacin |
| contig00296 | 404 | 1368 | ant(3’’)-Ia_1 | 3/7 | 99.3 | 99.1 | X02340 | ant(3’’)-Ia | Streptomycin |
| contig00121 | 8734 | 9537 | aph(3’’)-Ib_5 | 0/0 | 100.0 | 100.0 | AF321551 | aph(3’’)-Ib | Streptomycin |
| contig00121 | 7898 | 8734 | aph(6)-Id_1 | 0/0 | 100.0 | 100.0 | M28829 | aph(6)-Id | Streptomycin |
| contig00121 | 2620 | 3495 | blaCTX-M-15_1 | 0/0 | 100.0 | 100.0 | AY044436 | blaCTX-M-15 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin |
| contig00075 | 17699 | 18844 | blaMIR-5_1 | 0/0 | 100.0 | 100.0 | FJ237367 | blaMIR-5 | |
| contig00261 | 578 | 1408 | blaOXA-1_1 | 0/0 | 100.0 | 100.0 | HQ170510 | blaOXA-1 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig00121 | 6317 | 7177 | blaTEM-1B_1 | 0/0 | 100.0 | 100.0 | AY458016 | blaTEM-1B | Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin |
| contig00313 | 350 | 1004 | catA1_1 | 0/0 | 99.2 | 99.8 | V00622 | catA1 | Chloramphenicol |
| contig00180 | 3154 | 3627 | dfrA1_8 | 0/0 | 100.0 | 100.0 | X00926 | dfrA1 | Trimethoprim |
| contig00311 | 442 | 924 | dfrA14_5 | 0/0 | 100.0 | 99.6 | DQ388123 | dfrA14 | Trimethoprim |
| contig00175 | 4912 | 5337 | fosA_7 | 0/0 | 100.0 | 97.0 | AEXB01000013 | fosA | Fosfomycin |
| contig00193 | 4172 | 5093 | mph(A)_2 | 1/1 | 100.0 | 99.6 | U36578 | mph(A) | Erythromycin, Azithromycin, Spiramycin, Telithromycin |
| contig00185 | 4403 | 5047 | qnrB1_1 | 0/0 | 100.0 | 100.0 | DQ351241 | qnrB1 | Ciprofloxacin |
| contig00180 | 1270 | 2136 | sul1_5 | 0/0 | 100.0 | 99.9 | EU780013 | sul1 | Sulfamethoxazole |
| contig00121 | 9598 | 10413 | sul2_2 | 0/0 | 100.0 | 100.0 | AY034138 | sul2 | Sulfamethoxazole |
| contig00219 | 1429 | 2697 | tet(A)_6 | 1/22 | 97.8 | 93.2 | AF534183 | tet(A) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00250 | 1696 | 2556 | AAC(3)-IIe | 0/0 | 100.0 | 99.5 | EU022315.1:0-861 | AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli | aminoglycoside |
| contig00261 | 1539 | 2138 | AAC(6’)-Ib-cr | 0/0 | 100.0 | 100.0 | DQ303918:0-600 | AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously | aminoglycoside, fluoroquinolone |
| contig00296 | 404 | 1368 | ANT(3’’)-IIa | 3/7 | 99.3 | 99.1 | X02340.1:222-1194 | ANT(3’’)-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms. | aminoglycoside |
| contig00121 | 8734 | 9537 | APH(3’’)-Ib | 0/0 | 100.0 | 99.8 | AF313472:15593-16397 | APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. | aminoglycoside |
| contig00121 | 7898 | 8734 | APH(6)-Id | 0/0 | 100.0 | 99.9 | AF024602:3155-3992 | APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum | aminoglycoside |
| contig00313 | 350 | 1004 | catI | 0/0 | 99.2 | 99.8 | V00622:243-903 | catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii | phenicol |
| contig00121 | 2620 | 3495 | CTX-M-15 | 0/0 | 100.0 | 100.0 | AY044436:1435-2311 | CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family | cephalosporin |
| contig00180 | 3154 | 3627 | dfrA1 | 0/0 | 100.0 | 99.8 | KJ541681.1:19526-20000 | dfrA1 is an integron-encoded dihydrofolate reductase | diaminopyrimidine |
| contig00311 | 442 | 924 | dfrA14 | 0/0 | 100.0 | 99.8 | EU780012:2162-2645 | dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli | diaminopyrimidine |
| contig00104 | 6740 | 7933 | Enterobacter_cloacae_acrA | 0/0 | 100.0 | 99.6 | DQ679966:299-1493 | AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae. | cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan |
| contig00175 | 4912 | 5337 | FosA2 | 0/0 | 100.0 | 92.2 | EU487198:216-642 | An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. | fosfomycin |
| contig00075 | 17699 | 18844 | MIR-23 | 0/0 | 100.0 | 99.7 | KJ949106.1:0-1146 | MIR-23 originally described as AZECL-25 is a class C beta-lactamase that is found in Enterobacter cloacae. | cephalosporin, monobactam |
| contig00193 | 4172 | 5077 | mphA | 0/0 | 100.0 | 99.9 | D16251.1:2531-1625 | The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner. | macrolide |
| contig00261 | 578 | 1408 | OXA-1 | 0/0 | 100.0 | 100.0 | JN420336.1:2230-1399 | OXA-1 is a beta-lactamase found in E. coli | cephalosporin, penam |
| contig00223 | 725 | 1057 | qacH | 0/0 | 100.0 | 99.7 | DQ149925.1:188-521 | qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae | fluoroquinolone |
| contig00185 | 4366 | 5047 | QnrB17 | 1/1 | 100.0 | 99.1 | AM919398:0-681 | QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii | fluoroquinolone |
| contig00066 | 19789 | 20140 | ramA | 0/0 | 93.9 | 93.2 | JQ727668:0-375 | RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. | carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan |
| contig00180 | 3754 | 4611 | RSA-1 | 0/0 | 100.0 | 99.8 | MG739510.1:0-858 | RSA-1 is a class A beta-lactamase resistance enzyme identified from a functional metagenomic study of contaminated river sediments. | carbapenem, cephalosporin |
| contig00180 | 1270 | 2109 | sul1 | 0/0 | 100.0 | 100.0 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig00121 | 9598 | 10413 | sul2 | 0/0 | 100.0 | 100.0 | AY055428.1:21084-20268 | Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. | sulfonamide |
| contig00121 | 6317 | 7177 | TEM-1 | 0/0 | 100.0 | 99.9 | AL513383:161910-162771 | TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. | cephalosporin, monobactam, penam, penem |
| contig00219 | 1429 | 2697 | tet(A) | 1/22 | 97.8 | 93.2 | AF534183.1:2970-4245 | TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00250 | 1696 | 2556 | (AGly)aac3-IIa | 0/0 | 100.0 | 99.8 | X51534:91-951 | (AGly)aac3-IIa | NA |
| contig00296 | 404 | 1215 | (AGly)aadA1-pm | 0/0 | 97.7 | 99.9 | JQ690540:7968-8798 | (AGly)aadA1-pm | NA |
| contig00121 | 8734 | 9537 | (AGly)strA | 0/0 | 100.0 | 99.9 | AB366441:22458-23261 | (AGly)strA | NA |
| contig00121 | 7898 | 8734 | (AGly)strB | 0/0 | 100.0 | 100.0 | FJ474091:264-1100 | (AGly)strB | NA |
| contig00121 | 2620 | 3495 | (Bla)blaCTX-M-15 | 0/0 | 100.0 | 100.0 | JQ686199:261-1136 | (Bla)blaCTX-M-15 | NA |
| contig00075 | 17699 | 18844 | (Bla)blaMIR-5 | 0/0 | 100.0 | 100.0 | FJ237367:1-1146 | (Bla)blaMIR-5 | NA |
| contig00261 | 578 | 1408 | (Bla)blaOXA-1 | 0/0 | 100.0 | 100.0 | JQ682867:1-831 | (Bla)blaOXA-1 | NA |
| contig00121 | 6317 | 7177 | (Bla)blaTEM-105 | 0/0 | 100.0 | 99.9 | AF516720:215-1075 | (Bla)blaTEM-105 | NA |
| contig00175 | 4912 | 5337 | (Fcyn)FosA2 | 0/0 | 100.0 | 92.2 | EU487198:217-642 | (Fcyn)FosA2 | NA |
| contig00185 | 4366 | 5047 | (Flq)qnrB1 | 1/1 | 100.0 | 99.8 | DQ351241:1-681 | (Flq)qnrB1 | NA |
| contig00193 | 4172 | 5077 | (MLS)mph(A) | 0/0 | 100.0 | 99.9 | DQ445270:1626-2531 | (MLS)mph(A) | NA |
| contig00313 | 350 | 1004 | (Phe)catA1 | 0/0 | 99.2 | 99.8 | V00622:244-903 | (Phe)catA1 | NA |
| contig00180 | 1270 | 2109 | (Sul)sul1 | 0/0 | 100.0 | 100.0 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig00121 | 9598 | 10413 | (Sul)sul2 | 0/0 | 100.0 | 100.0 | EU360945:1617-2432 | (Sul)sul2 | NA |
| contig00219 | 1429 | 2725 | (Tet)tetA | 1/22 | 100.0 | 93.3 | JX424423:94438-95712 | (Tet)tetA | NA |
| contig00219 | 757 | 1398 | (Tet)tetR | 1/9 | 98.6 | 93.1 | HF545434:53576-54226 | (Tet)tetR | NA |
| contig00180 | 3154 | 3627 | (Tmt)dfrA1 | 0/0 | 100.0 | 100.0 | JQ794607:474 | (Tmt)dfrA1 | NA |
| contig00311 | 442 | 915 | (Tmt)dfrA14 | 0/0 | 100.0 | 100.0 | GU726917:72-545 | (Tmt)dfrA14 | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00250 | 1696 | 2556 | aac(3)-IIe | 0/0 | 100.0 | 99.8 | NG_047244.1 | aminoglycoside N-acetyltransferase AAC(3)-IIe | GENTAMICIN |
| contig00261 | 1539 | 2093 | aac(6’)-Ib-D181Y | 0/0 | 100.0 | 99.8 | NG_067946.1 | AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase | AMIKACIN, KANAMYCIN, TOBRAMYCIN |
| contig00296 | 404 | 1195 | aadA1 | 0/0 | 100.0 | 100.0 | NG_052536.1 | ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 | STREPTOMYCIN |
| contig00121 | 8734 | 9561 | aph(3’’)-Ib | 0/0 | 100.0 | 100.0 | NG_056002.2 | aminoglycoside O-phosphotransferase APH(3’’)-Ib | STREPTOMYCIN |
| contig00121 | 7898 | 8734 | aph(6)-Id | 0/0 | 100.0 | 100.0 | NG_047464.1 | aminoglycoside O-phosphotransferase APH(6)-Id | STREPTOMYCIN |
| contig00121 | 2620 | 3495 | blaCTX-M-15 | 0/0 | 100.0 | 100.0 | NG_048935.1 | class A extended-spectrum beta-lactamase CTX-M-15 | CEPHALOSPORIN |
| contig00075 | 17699 | 18844 | blaMIR-5 | 0/0 | 100.0 | 100.0 | NG_049306.1 | cephalosporin-hydrolyzing class C beta-lactamase MIR-5 | CEPHALOSPORIN |
| contig00261 | 578 | 1408 | blaOXA-1 | 0/0 | 100.0 | 100.0 | NG_049392.1 | oxacillin-hydrolyzing class D beta-lactamase OXA-1 | CEPHALOSPORIN |
| contig00121 | 6317 | 7177 | blaTEM-1 | 0/0 | 100.0 | 100.0 | NG_050145.1 | class A broad-spectrum beta-lactamase TEM-1 | BETA-LACTAM |
| contig00313 | 350 | 1004 | catA1 | 0/0 | 99.2 | 99.8 | NG_047582.1 | type A-1 chloramphenicol O-acetyltransferase | CHLORAMPHENICOL |
| contig00180 | 3154 | 3627 | dfrA1 | 0/0 | 100.0 | 100.0 | NG_047676.1 | trimethoprim-resistant dihydrofolate reductase DfrA1 | TRIMETHOPRIM |
| contig00311 | 442 | 915 | dfrA14 | 0/0 | 100.0 | 100.0 | NG_056035.1 | trimethoprim-resistant dihydrofolate reductase DfrA14 | TRIMETHOPRIM |
| contig00175 | 4912 | 5337 | fosA | 0/0 | 100.0 | 96.5 | NG_050405.1 | fosfomycin resistance glutathione transferase FosA | FOSFOMYCIN |
| contig00193 | 4172 | 5093 | mph(A) | 1/1 | 100.0 | 99.6 | NG_047986.1 | Mph(A) family macrolide 2’-phosphotransferase | MACROLIDE |
| contig00053 | 19028 | 22147 | oqxB9 | 0/0 | 99.0 | 90.2 | NG_050458.1 | multidrug efflux RND transporter permease subunit OqxB9 | PHENICOL, QUINOLONE |
| contig00185 | 4403 | 5047 | qnrB1 | 0/0 | 100.0 | 100.0 | NG_050469.1 | quinolone resistance pentapeptide repeat protein QnrB1 | QUINOLONE |
| contig00180 | 1270 | 2109 | sul1 | 0/0 | 100.0 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| contig00121 | 9598 | 10413 | sul2 | 0/0 | 100.0 | 100.0 | NG_051852.1 | sulfonamide-resistant dihydropteroate synthase Sul2 | SULFONAMIDE |
| contig00219 | 1526 | 2725 | tet(A) | 0/0 | 100.0 | 100.0 | NG_048157.1 | tetracycline efflux MFS transporter Tet(A) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00250 | 1696 | 2556 | AAC3 | 0/0 | 100.0 | 99.8 | MEG_44 | Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 | NA |
| contig00104 | 6740 | 7933 | ACRB | 0/0 | 100.0 | 99.6 | MEG_402 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB | NA |
| contig00296 | 404 | 1368 | ANT3-DPRIME | 3/7 | 99.3 | 99.1 | MEG_949 | Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME | NA |
| contig00121 | 8734 | 9561 | APH3-DPRIME | 0/0 | 100.0 | 100.0 | MEG_1019 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME | NA |
| contig00121 | 7898 | 8734 | APH6 | 0/0 | 100.0 | 100.0 | MEG_1086 | Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 | NA |
| contig00313 | 339 | 1004 | CATA | 0/0 | 99.2 | 100.0 | MEG_1593 | Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA | NA |
| contig00320 | 62 | 1004 | CTX | 0/0 | 100.0 | 99.0 | MEG_2435 | Drugs:betalactams:Class_A_betalactamases:CTX | NA |
| contig00180 | 3154 | 3627 | DFRA | 0/0 | 100.0 | 99.8 | MEG_2495 | Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA | NA |
| contig00311 | 442 | 915 | DFRA | 0/0 | 100.0 | 99.8 | MEG_2517 | Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA | NA |
| contig00175 | 4912 | 5493 | FOSA | 0/0 | 100.0 | 92.8 | MEG_2990 | Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA | NA |
| contig00075 | 17699 | 18844 | MIR | 0/0 | 100.0 | 100.0 | MEG_3959 | Drugs:betalactams:Class_C_betalactamases:MIR | NA |
| contig00193 | 4172 | 5093 | MPHA | 1/1 | 100.0 | 99.6 | MEG_4030 | Drugs:MLS:Macrolide_phosphotransferases:MPHA | NA |
| contig00053 | 19028 | 22147 | OQXB | 0/0 | 99.0 | 90.2 | MEG_4359 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB | NA |
| contig00261 | 578 | 1408 | OXA | 0/0 | 100.0 | 100.0 | MEG_4980 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00223 | 725 | 1057 | QACF | 0/0 | 100.0 | 100.0 | MEG_5833 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACF | NA |
| contig00185 | 4366 | 5047 | QNRB | 1/1 | 100.0 | 99.1 | MEG_5928 | Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB | NA |
| contig00066 | 19789 | 20140 | RAMA | 0/0 | 93.9 | 93.2 | MEG_6044 | Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA | NA |
| contig00180 | 3754 | 4611 | RSA | 0/0 | 100.0 | 99.8 | MEG_6149 | Drugs:betalactams:Class_A_betalactamases:RSA | NA |
| contig00180 | 1143 | 2110 | SULI | 0/0 | 100.0 | 100.0 | MEG_6615 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI | NA |
| contig00121 | 9598 | 10413 | SULII | 0/0 | 100.0 | 100.0 | MEG_6617 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII | NA |
| contig00121 | 5950 | 7195 | TEM | 0/0 | 98.3 | 99.4 | MEG_6875 | Drugs:betalactams:Class_A_betalactamases:TEM | NA |
| contig00219 | 1526 | 2725 | TETA | 0/0 | 100.0 | 100.0 | MEG_7021 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA | NA |
## [1] "No antibiotic resistance genes from Resfinder database were found"
## [1] "No antibiotic resistance genes from CARD database were found"
## [1] "No antibiotic resistance genes from ARG-ANNOT database were found"
## [1] "No antibiotic resistance genes from NCBI database were found"
## [1] "No antibiotic resistance genes from MEGARES database were found"
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00278 | 783 | 1316 | ant(2’’)-Ia_1 | 0/0 | 100.0 | 100.0 | X04555 | ant(2’’)-Ia | Gentamicin, Tobramycin |
| contig00278 | 14 | 769 | blaDIM-1_1 | 0/0 | 100.0 | 100.0 | GU323019 | blaDIM-1 | |
| contig02287 | 111 | 928 | blaOXA-22_1 | 0/0 | 99.2 | 100.0 | AF064820 | blaOXA-22 | Amoxicillin, Ampicillin, Aztreonam, Cefepime, Piperacillin, Piperacillin+Tazobactam |
| contig01918 | 45 | 860 | blaOXA-60_1 | 0/0 | 100.0 | 100.0 | AF525303 | blaOXA-60 | Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Imipenem |
| contig01154 | 204 | 1463 | cmlA1_1 | 0/0 | 100.0 | 99.8 | M64556 | cmlA1 | Chloramphenicol |
| contig00362 | 1 | 817 | sul1_2 | 0/0 | 97.3 | 100.0 | U12338 | sul1 | Sulfamethoxazole |
| contig00005 | 833 | 2079 | tet(A)_6 | 0/0 | 97.8 | 100.0 | AF534183 | tet(A) | Doxycycline, Tetracycline |
| contig00462 | 874 | 2049 | tet(G)_2 | 0/0 | 100.0 | 99.9 | AF133140 | tet(G) | Doxycycline, Tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00278 | 783 | 1316 | ANT(2’’)-Ia | 0/0 | 100.0 | 100.0 | AF078527:3769-4303 | Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii | aminoglycoside |
| contig02083 | 33 | 485 | arr-2 | 0/0 | 100.0 | 100.0 | AF078527:4387-4840 | arr-2 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa | rifamycin |
| contig01154 | 204 | 1463 | cmlA6 | 0/0 | 100.0 | 100.0 | AF294653:2749-4009 | cmlA6 is a plasmid-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa | phenicol |
| contig00278 | 14 | 769 | DIM-1_beta-lactamase | 0/0 | 100.0 | 100.0 | KC004136:40-796 | Dutch imipenemase or DIM-1 is an integron-encoded metallo-beta-lactamase from Pseudomonas stutzeri | carbapenem, cephalosporin |
| contig02287 | 111 | 928 | OXA-22 | 0/0 | 99.2 | 100.0 | AF064820:951-1776 | OXA-22 is a beta-lactamase found in Ralstonia pickettii | cephalosporin, penam |
| contig01918 | 45 | 860 | OXA-60 | 0/0 | 100.0 | 100.0 | AF525303:2770-3586 | OXA-60 is a beta-lactamase found in Ralstonia pickettii | cephalosporin, penam |
| contig00278 | 1479 | 1811 | qacH | 0/0 | 100.0 | 91.6 | DQ149925.1:188-521 | qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae | fluoroquinolone |
| contig00362 | 1 | 817 | sul1 | 0/0 | 97.3 | 100.0 | JF969163:1053-1893 | Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. | sulfonamide |
| contig00005 | 833 | 2079 | tet(A) | 0/0 | 97.8 | 100.0 | AF534183.1:2970-4245 | TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. | tetracycline |
| contig00462 | 874 | 2049 | tet(G) | 0/0 | 100.0 | 92.9 | AF133139:0-1176 | TetG is a tetracycline efflux protein found in Gram-negative bacteria. The encoding gene is found in both chromosomal and plasmid DNA where it is frequently linked to the floR sul1 and cmlA9 genes which encode proteins that can confer florfenicol/chloramphenicol sulfamethoxazole and chloramphenicol resistance respectively. | tetracycline |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00278 | 783 | 1316 | (AGly)aadB | 0/0 | 100.0 | 100.0 | JQ690540:4275-4808 | (AGly)aadB | NA |
| contig00278 | 14 | 769 | (Bla)blaDIM-1 | 0/0 | 100.0 | 100.0 | GU323019:1-756 | (Bla)blaDIM-1 | NA |
| contig02287 | 111 | 928 | (Bla)blaOXA-22 | 0/0 | 99.2 | 100.0 | AF064820:952-1776 | (Bla)blaOXA-22 | NA |
| contig01918 | 45 | 860 | (Bla)blaOXA-60 | 0/0 | 100.0 | 93.1 | AY664505:1-816 | (Bla)blaOXA-60 | NA |
| contig01154 | 204 | 1463 | (Phe)cmlA6 | 0/0 | 100.0 | 100.0 | NG_047655:101-1360 | (Phe)cmlA6 | NA |
| contig02083 | 33 | 485 | (Rif)arr2 | 0/0 | 100.0 | 100.0 | JQ639792:1050-1502 | (Rif)arr2 | NA |
| contig00362 | 1 | 817 | (Sul)sul1 | 0/0 | 97.3 | 100.0 | AF071413:6700-7539 | (Sul)sul1 | NA |
| contig00005 | 833 | 2107 | (Tet)tetA | 0/0 | 100.0 | 100.0 | JX424423:94438-95712 | (Tet)tetA | NA |
| contig00462 | 874 | 2049 | (Tet)tetG | 0/0 | 100.0 | 99.9 | AF133140:757-1932 | (Tet)tetG | NA |
| contig00005 | 152 | 802 | (Tet)tetR | 0/0 | 100.0 | 100.0 | HF545434:53576-54226 | (Tet)tetR | NA |
| contig00462 | 2153 | 2761 | (Tet)tetR(G) | 0/0 | 96.2 | 98.5 | S52438:113-745 | (Tet)tetR(G) | NA |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig00278 | 783 | 1316 | ant(2’’)-Ia | 0/0 | 100.0 | 100.0 | NG_047387.1 | aminoglycoside nucleotidyltransferase ANT(2’’)-Ia | GENTAMICIN, KANAMYCIN, TOBRAMYCIN |
| contig02083 | 33 | 485 | arr-2 | 0/0 | 100.0 | 100.0 | NG_048580.1 | NAD(+)–rifampin ADP-ribosyltransferase Arr-2 | RIFAMYCIN |
| contig00278 | 14 | 769 | blaDIM-1 | 0/0 | 100.0 | 100.0 | NG_049077.1 | subclass B1 metallo-beta-lactamase DIM-1 | CARBAPENEM |
| contig02287 | 111 | 928 | blaOXA-22 | 0/0 | 99.2 | 100.0 | NG_049518.1 | benzylpenicillin-hydrolyzing class D beta-lactamase OXA-22 | BETA-LACTAM |
| contig01918 | 45 | 860 | blaOXA-60 | 0/0 | 100.0 | 100.0 | NG_049800.1 | carbapenem-hydrolyzing class D beta-lactamase OXA-60 | CARBAPENEM |
| contig01154 | 204 | 1463 | cmlA6 | 0/0 | 100.0 | 100.0 | NG_047655.1 | chloramphenicol efflux MFS transporter CmlA6 | CHLORAMPHENICOL |
| contig00462 | 2986 | 4200 | floR2 | 0/0 | 100.0 | 100.0 | NG_047875.1 | chloramphenicol/florfenicol efflux MFS transporter FloR2 | CHLORAMPHENICOL, FLORFENICOL |
| contig00362 | 1 | 817 | sul1 | 0/0 | 97.3 | 100.0 | NG_048082.1 | sulfonamide-resistant dihydropteroate synthase Sul1 | SULFONAMIDE |
| contig00005 | 908 | 2107 | tet(A) | 0/0 | 100.0 | 100.0 | NG_048154.1 | tetracycline efflux MFS transporter Tet(A) | TETRACYCLINE |
| contig00462 | 874 | 2049 | tet(G) | 0/0 | 100.0 | 99.9 | NG_051907.1 | tetracycline efflux MFS transporter Tet(G) | TETRACYCLINE |
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product | Resistance |
|---|---|---|---|---|---|---|---|---|---|
| contig01154 | 3 | 1463 | CMLA | 1/1 | 100.0 | 99.6 | MEG_1768 | Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:CMLA | NA |
| contig00278 | 14 | 769 | DIM | 0/0 | 100.0 | 100.0 | MEG_2649 | Drugs:betalactams:Class_B_betalactamases:DIM | NA |
| contig00462 | 2986 | 4200 | FLOR | 0/0 | 100.0 | 100.0 | MEG_2912 | Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR | NA |
| contig01918 | 45 | 860 | OXA | 0/0 | 100.0 | 100.0 | MEG_4779 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig02287 | 111 | 928 | OXA | 0/0 | 99.2 | 100.0 | MEG_4766 | Drugs:betalactams:Class_D_betalactamases:OXA | NA |
| contig00278 | 1479 | 1811 | QACL | 0/0 | 100.0 | 100.0 | MEG_5852 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACL | NA |
| contig00362 | 1 | 944 | SULI | 0/0 | 97.5 | 100.0 | MEG_6615 | Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI | NA |
| contig00005 | 833 | 2107 | TETA | 0/0 | 100.0 | 100.0 | MEG_7024 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA | NA |
| contig00462 | 874 | 2049 | TETG | 0/0 | 100.0 | 99.9 | MEG_7077 | Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETG | NA |
| contig00079 | 8019 | 9173 | TTGA | 0/0 | 100.0 | 90.0 | MEG_7287 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:TTGA | NA |
| contig00079 | 9177 | 12329 | TTGB | 0/0 | 100.0 | 92.0 | MEG_7288 | Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:TTGB | NA |
Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample
| Field | Description |
|---|---|
| Contig | Contig name where the gene was found |
| Start | Start position of the gene within the contig |
| End | End position of the gene within the contig |
| Gene | Antibiotic resistance gene |
| Gaps | Gaps in subject (genome) and query (antibiotic resistance gene) |
| Coverage | Proportion (%) of the gene covered |
| Identity | Proportion (%) of exact nucleotide matches |
| Accession | Accesion number of the antibiotic resistance gene |
| Product | Antibiotic resistance gene product |
## [1] "NO PLASMID FOUND!!"
## [1] "NO PLASMID FOUND!!"
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00364 | 768 | 1155 | IncFIA_1 | 0/0 | 100 | 99.7 | AP001918 | IncFIA_1__AP001918 |
| contig00403 | 832 | 1513 | IncFIB(AP001918)_1 | 0/0 | 100 | 98.2 | AP001918 | IncFIB(AP001918)_1__AP001918 |
## [1] "NO PLASMID FOUND!!"
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00085 | 400 | 632 | Col(BS512)_1 | 0/0 | 100 | 100.0 | NC_010656 | Col(BS512)_1__NC_010656 |
| contig00090 | 1071 | 1332 | Col(MG828)_1 | 0/0 | 100 | 93.1 | NC_008486 | Col(MG828)_1__NC_008486 |
| contig00067 | 5514 | 5644 | ColRNAI_1 | 1/1 | 100 | 90.1 | DQ298019 | ColRNAI_1__DQ298019 |
| contig00068 | 3818 | 4582 | IncY_1 | 0/0 | 100 | 98.8 | K02380 | IncY_1__K02380 |
## [1] "NO PLASMID FOUND!!"
## [1] "NO PLASMID FOUND!!"
## [1] "NO PLASMID FOUND!!"
## [1] "NO PLASMID FOUND!!"
## [1] "NO PLASMID FOUND!!"
| Contig | Start | End | Gene | Gaps | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00003 | 81165 | 81491 | IncHI2_1 | 0/0 | 100 | 100.0 | BX664015 | IncHI2_1__BX664015 |
| contig00003 | 96357 | 96986 | IncHI2A_1 | 0/0 | 100 | 100.0 | BX664015 | IncHI2A_1__BX664015 |
| contig00149 | 883 | 1133 | IncR_1 | 0/0 | 100 | 99.6 | DQ449578 | IncR_1__DQ449578 |
## [1] "NO PLASMID FOUND!!"
## [1] "NO PLASMID FOUND!!"
| Field | Description |
|---|---|
| Contig | Contig name where the gene was found |
| Start | Start position of the gene within the contig |
| End | End position of the gene within the contig |
| Gene | Antibiotic resistance gene |
| Coverage | Proportion (%) of the gene covered |
| Identity | Proportion (%) of exact nucleotide matches |
| Accession | Accesion number of the antibiotic resistance gene |
| Product | Antibiotic resistance gene product |
## Error in read.table("ID003II_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
## Error in as.data.frame(vfdb): object 'vfdb' not found
## Error in cbind(vfdb[, 1:9]): object 'vfdb' not found
## Error in colnames(vfdbdata) = c("Contig", "Start", "End", "Strand", "Gene", : object 'vfdbdata' not found
## Error in eval(expr, envir, enclos): object 'vfdb' not found
## Error in row.names(vfdb) = NULL: object 'vfdb' not found
## Error in nrow(vfdb): object 'vfdb' not found
## Error in read.table("ID012II_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
## Error in as.data.frame(vfdb): object 'vfdb' not found
## Error in cbind(vfdb[, 1:9]): object 'vfdb' not found
## Error in colnames(vfdbdata) = c("Contig", "Start", "End", "Strand", "Gene", : object 'vfdbdata' not found
## Error in eval(expr, envir, enclos): object 'vfdb' not found
## Error in row.names(vfdb) = NULL: object 'vfdb' not found
## Error in nrow(vfdb): object 'vfdb' not found
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00017 | 34037 | 35465 | - | aslA | 100.0 | 93.6 | AAG10151 | (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00179 | 6301 | 6756 | - | csgB | 99.8 | 83.8 | NP_460114 | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00179 | 7511 | 8161 | + | csgD | 100.0 | 81.1 | NP_460113 | (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00179 | 8580 | 8996 | + | csgF | 99.0 | 81.2 | NP_460111 | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00179 | 9023 | 9856 | + | csgG | 100.0 | 83.5 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00088 | 15712 | 16458 | - | entA | 100.0 | 95.7 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 16458 | 17315 | - | entB | 100.0 | 98.1 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 18949 | 20136 | - | entC | 100.0 | 97.9 | NP_752611 | (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00320 | 107 | 877 | - | entD | 100.0 | 95.2 | NP_752599 | (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 17329 | 18939 | - | entE | 100.0 | 95.5 | NP_752612 | (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 26999 | 30196 | - | entF | 82.4 | 95.5 | NP_752604 | (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 21459 | 22709 | - | entS | 100.0 | 95.4 | NP_752609 | (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00184 | 2194 | 4093 | + | espL1 | 100.0 | 97.6 | NP_288154 | (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00072 | 27898 | 30084 | + | espL4 | 100.0 | 97.3 | NP_290644 | (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00116 | 21550 | 22603 | + | espR1 | 83.7 | 93.8 | NP_287686 | (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00194 | 10350 | 11484 | + | espR4 | 99.5 | 84.3 | NP_288396 | (espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00065 | 33331 | 34752 | - | espX1 | 100.0 | 93.2 | NP_285716 | (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00251 | 287 | 1867 | + | espX4 | 99.9 | 93.2 | NP_290672 | (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00238 | 7154 | 8446 | - | espX5 | 100.0 | 97.1 | NP_290699 | (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00039 | 24795 | 25606 | - | espY1 | 99.9 | 87.0 | NP_285753 | (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00320 | 902 | 3142 | - | fepA | 100.0 | 96.7 | NP_752600 | (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 20499 | 21455 | + | fepB | 100.0 | 97.5 | NP_752610 | (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 24810 | 25625 | + | fepC | 100.0 | 97.3 | NP_752606 | (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 22808 | 23824 | + | fepD | 100.0 | 96.1 | NP_752608 | (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 23821 | 24813 | + | fepG | 100.0 | 94.1 | NP_752607 | (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00320 | 3385 | 4587 | + | fes | 100.0 | 96.7 | NP_752602 | (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00100 | 25238 | 25849 | - | fimA | 100.0 | 88.6 | NP_757241 | (fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00270 | 1070 | 1672 | - | fimB | 100.0 | 98.2 | NP_757239 | (fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 23872 | 24597 | - | fimC | 100.0 | 98.9 | NP_757243 | (fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 21169 | 23805 | - | fimD | 100.0 | 98.6 | NP_757244 | (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00270 | 1 | 593 | - | fimE | 99.3 | 99.3 | NP_757240 | (fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 20629 | 21162 | - | fimF | 100.0 | 97.9 | NP_757245 | (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 20113 | 20616 | - | fimG | 100.0 | 97.8 | NP_757247 | (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 19191 | 20102 | - | fimH | 100.0 | 97.4 | NP_757248 | (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 24634 | 25173 | - | fimI | 100.0 | 98.7 | NP_757242 | (fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00230 | 2728 | 4749 | + | fyuA | 100.0 | 99.9 | NP_405467 | (fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00016 | 7662 | 8492 | + | gspC | 100.0 | 94.7 | YP_404599 | (gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 8732 | 10582 | + | gspD | 100.0 | 96.1 | YP_404600 | (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 10582 | 12075 | + | gspE | 100.0 | 96.9 | YP_404601 | (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 12075 | 13274 | + | gspF | 100.0 | 96.0 | YP_404602 | (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 13315 | 13770 | + | gspG | 100.0 | 95.0 | YP_404603 | (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 13807 | 14336 | + | gspH | 99.8 | 94.9 | YP_404604 | (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 14333 | 14704 | + | gspI | 100.0 | 94.9 | YP_404605 | (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 14737 | 15306 | + | gspJ | 100.0 | 96.7 | YP_404606 | (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 15303 | 16280 | + | gspK | 100.0 | 97.0 | YP_404607 | (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 16595 | 17455 | + | gspL | 100.0 | 97.0 | YP_404608 | (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 17571 | 17993 | + | gspM | 100.0 | 98.3 | YP_404609 | (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00109 | 15615 | 21722 | + | irp2 | 100.0 | 99.8 | NP_405472 | (irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00300 | 4506 | 5546 | - | ompA | 100.0 | 98.1 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00109 | 14465 | 15424 | + | ybtA | 100.0 | 99.5 | NP_405473 | (ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00230 | 1020 | 2597 | + | ybtE | 100.0 | 99.8 | NP_405468 | (ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 12496 | 14298 | - | ybtP | 100.0 | 99.6 | NP_405474 | (ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 10707 | 12509 | - | ybtQ | 100.0 | 99.7 | NP_405475 | (ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 8102 | 9406 | - | ybtS | 100.0 | 99.9 | NP_405477 | (ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00230 | 213 | 1016 | + | ybtT | 100.0 | 99.8 | NP_405469 | (ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 9434 | 10714 | - | ybtX | 100.0 | 99.7 | NP_405476 | (ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
## Error in read.table("ID030_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00017 | 34037 | 35465 | - | aslA | 100.0 | 93.6 | AAG10151 | (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00179 | 6301 | 6756 | - | csgB | 99.8 | 83.8 | NP_460114 | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00179 | 7511 | 8161 | + | csgD | 100.0 | 81.1 | NP_460113 | (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00179 | 8580 | 8996 | + | csgF | 99.0 | 81.2 | NP_460111 | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00179 | 9023 | 9856 | + | csgG | 100.0 | 83.5 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00088 | 15712 | 16458 | - | entA | 100.0 | 95.7 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 16458 | 17315 | - | entB | 100.0 | 98.1 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 18949 | 20136 | - | entC | 100.0 | 97.9 | NP_752611 | (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00320 | 107 | 877 | - | entD | 100.0 | 95.2 | NP_752599 | (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 17329 | 18939 | - | entE | 100.0 | 95.5 | NP_752612 | (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 26999 | 30196 | - | entF | 82.4 | 95.5 | NP_752604 | (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 21459 | 22709 | - | entS | 100.0 | 95.4 | NP_752609 | (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00184 | 2194 | 4093 | + | espL1 | 100.0 | 97.6 | NP_288154 | (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00072 | 27898 | 30084 | + | espL4 | 100.0 | 97.3 | NP_290644 | (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00116 | 21550 | 22603 | + | espR1 | 83.7 | 93.8 | NP_287686 | (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00194 | 10350 | 11484 | + | espR4 | 99.5 | 84.3 | NP_288396 | (espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00065 | 33331 | 34752 | - | espX1 | 100.0 | 93.2 | NP_285716 | (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00251 | 287 | 1867 | + | espX4 | 99.9 | 93.2 | NP_290672 | (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00238 | 7154 | 8446 | - | espX5 | 100.0 | 97.1 | NP_290699 | (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00039 | 24795 | 25606 | - | espY1 | 99.9 | 87.0 | NP_285753 | (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00320 | 902 | 3142 | - | fepA | 100.0 | 96.7 | NP_752600 | (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 20499 | 21455 | + | fepB | 100.0 | 97.5 | NP_752610 | (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 24810 | 25625 | + | fepC | 100.0 | 97.3 | NP_752606 | (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 22808 | 23824 | + | fepD | 100.0 | 96.1 | NP_752608 | (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00088 | 23821 | 24813 | + | fepG | 100.0 | 94.1 | NP_752607 | (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00320 | 3385 | 4587 | + | fes | 100.0 | 96.7 | NP_752602 | (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00100 | 25238 | 25849 | - | fimA | 100.0 | 88.6 | NP_757241 | (fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00270 | 1070 | 1672 | - | fimB | 100.0 | 98.2 | NP_757239 | (fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 23872 | 24597 | - | fimC | 100.0 | 98.9 | NP_757243 | (fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 21169 | 23805 | - | fimD | 100.0 | 98.6 | NP_757244 | (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00270 | 1 | 593 | - | fimE | 99.3 | 99.3 | NP_757240 | (fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 20629 | 21162 | - | fimF | 100.0 | 97.9 | NP_757245 | (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 20113 | 20616 | - | fimG | 100.0 | 97.8 | NP_757247 | (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 19191 | 20102 | - | fimH | 100.0 | 97.4 | NP_757248 | (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00100 | 24634 | 25173 | - | fimI | 100.0 | 98.7 | NP_757242 | (fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00230 | 2728 | 4749 | + | fyuA | 100.0 | 99.9 | NP_405467 | (fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00016 | 7662 | 8492 | + | gspC | 100.0 | 94.7 | YP_404599 | (gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 8732 | 10582 | + | gspD | 100.0 | 96.1 | YP_404600 | (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 10582 | 12075 | + | gspE | 100.0 | 96.9 | YP_404601 | (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 12075 | 13274 | + | gspF | 100.0 | 96.0 | YP_404602 | (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 13315 | 13770 | + | gspG | 100.0 | 95.0 | YP_404603 | (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 13807 | 14336 | + | gspH | 99.8 | 94.9 | YP_404604 | (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 14333 | 14704 | + | gspI | 100.0 | 94.9 | YP_404605 | (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 14737 | 15306 | + | gspJ | 100.0 | 96.7 | YP_404606 | (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 15303 | 16280 | + | gspK | 100.0 | 97.0 | YP_404607 | (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 16595 | 17455 | + | gspL | 100.0 | 97.0 | YP_404608 | (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00016 | 17571 | 17993 | + | gspM | 100.0 | 98.3 | YP_404609 | (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00109 | 15615 | 21722 | + | irp2 | 100.0 | 99.8 | NP_405472 | (irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00300 | 4506 | 5546 | - | ompA | 100.0 | 98.1 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00109 | 14465 | 15424 | + | ybtA | 100.0 | 99.5 | NP_405473 | (ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00230 | 1020 | 2597 | + | ybtE | 100.0 | 99.8 | NP_405468 | (ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 12496 | 14298 | - | ybtP | 100.0 | 99.6 | NP_405474 | (ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 10707 | 12509 | - | ybtQ | 100.0 | 99.7 | NP_405475 | (ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 8102 | 9406 | - | ybtS | 100.0 | 99.9 | NP_405477 | (ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00230 | 213 | 1016 | + | ybtT | 100.0 | 99.8 | NP_405469 | (ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| contig00109 | 9434 | 10714 | - | ybtX | 100.0 | 99.7 | NP_405476 | (ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92] |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00023 | 35665 | 37093 | + | aslA | 100.0 | 92.9 | AAG10151 | (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00005 | 153477 | 153932 | + | csgB | 99.8 | 83.6 | NP_460114 | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 152072 | 152722 | - | csgD | 100.0 | 81.3 | NP_460113 | (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 151237 | 151653 | - | csgF | 99.0 | 81.2 | NP_460111 | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 150377 | 151210 | - | csgG | 100.0 | 83.5 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00012 | 99370 | 100116 | - | entA | 100.0 | 95.7 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00099 | 257 | 1003 | + | entA | 100.0 | 98.4 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 100116 | 100973 | - | entB | 100.0 | 98.0 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 102607 | 103794 | - | entC | 100.0 | 97.9 | NP_752611 | (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 105 | 875 | - | entD | 100.0 | 95.2 | NP_752599 | (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 100987 | 102597 | - | entE | 100.0 | 95.4 | NP_752612 | (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 4803 | 8656 | + | entF | 99.3 | 95.6 | NP_752604 | (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 105117 | 106367 | - | entS | 100.0 | 95.4 | NP_752609 | (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00003 | 88782 | 90681 | - | espL1 | 100.0 | 97.6 | NP_288154 | (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 88201 | 90387 | + | espL4 | 100.0 | 97.3 | NP_290644 | (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00015 | 12139 | 13193 | - | espR1 | 83.7 | 94.1 | NP_287686 | (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00013 | 102593 | 104013 | + | espX1 | 99.9 | 95.3 | NP_285716 | (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 58405 | 59985 | - | espX4 | 100.0 | 96.5 | NP_290672 | (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 27599 | 28891 | + | espX5 | 100.0 | 97.0 | NP_290699 | (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00013 | 63516 | 64327 | - | espY1 | 99.9 | 87.0 | NP_285753 | (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 78302 | 82550 | - | fdeC | 99.9 | 94.2 | YP_002390132 | (fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88] |
| contig00066 | 900 | 3140 | - | fepA | 100.0 | 96.7 | NP_752600 | (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 104157 | 105113 | + | fepB | 100.0 | 97.5 | NP_752610 | (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 108468 | 109283 | + | fepC | 100.0 | 97.3 | NP_752606 | (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 106466 | 107482 | + | fepD | 100.0 | 96.1 | NP_752608 | (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 107479 | 108471 | + | fepG | 100.0 | 94.1 | NP_752607 | (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 3383 | 4585 | + | fes | 100.0 | 96.7 | NP_752602 | (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00050 | 21169 | 23555 | - | fimD | 90.5 | 98.7 | NP_757244 | (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 20629 | 21162 | - | fimF | 100.0 | 97.9 | NP_757245 | (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 20113 | 20616 | - | fimG | 100.0 | 97.8 | NP_757247 | (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 19191 | 20102 | - | fimH | 100.0 | 97.5 | NP_757248 | (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00035 | 903 | 2753 | + | gspD | 100.0 | 97.0 | YP_404600 | (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 2753 | 4246 | + | gspE | 100.0 | 96.5 | YP_404601 | (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 4246 | 5445 | + | gspF | 100.0 | 96.0 | YP_404602 | (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 5486 | 5941 | + | gspG | 100.0 | 95.0 | YP_404603 | (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 5978 | 6508 | + | gspH | 100.0 | 95.3 | YP_404604 | (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 6505 | 6876 | + | gspI | 100.0 | 95.2 | YP_404605 | (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 6909 | 7478 | + | gspJ | 100.0 | 96.7 | YP_404606 | (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 7475 | 8452 | + | gspK | 100.0 | 96.7 | YP_404607 | (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 8767 | 9627 | + | gspL | 100.0 | 97.1 | YP_404608 | (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 9743 | 10165 | + | gspM | 100.0 | 97.9 | YP_404609 | (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00005 | 69490 | 70530 | - | ompA | 100.0 | 98.1 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00006 | 91657 | 92410 | + | yagV/ecpE | 99.7 | 97.1 | NP_286006 | (yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 90090 | 91733 | + | yagW/ecpD | 100.0 | 99.1 | NP_286007 | (yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 87575 | 90100 | + | yagX/ecpC | 100.0 | 98.8 | NP_286008 | (yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 86881 | 87549 | + | yagY/ecpB | 100.0 | 98.1 | NP_286009 | (yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 86236 | 86823 | + | yagZ/ecpA | 100.0 | 99.0 | NP_286010 | (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 85571 | 86161 | + | ykgK/ecpR | 100.0 | 97.0 | NP_286011 | (ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
## Error in read.table("ID089_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00023 | 35665 | 37093 | + | aslA | 100.0 | 92.9 | AAG10151 | (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00005 | 153477 | 153932 | + | csgB | 99.8 | 83.6 | NP_460114 | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 152072 | 152722 | - | csgD | 100.0 | 81.3 | NP_460113 | (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 151237 | 151653 | - | csgF | 99.0 | 81.2 | NP_460111 | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 150377 | 151210 | - | csgG | 100.0 | 83.5 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00012 | 99370 | 100116 | - | entA | 100.0 | 95.7 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00099 | 257 | 1003 | + | entA | 100.0 | 98.4 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 100116 | 100973 | - | entB | 100.0 | 98.0 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 102607 | 103794 | - | entC | 100.0 | 97.9 | NP_752611 | (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 105 | 875 | - | entD | 100.0 | 95.2 | NP_752599 | (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 100987 | 102597 | - | entE | 100.0 | 95.4 | NP_752612 | (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 4803 | 8656 | + | entF | 99.3 | 95.6 | NP_752604 | (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 105117 | 106367 | - | entS | 100.0 | 95.4 | NP_752609 | (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00003 | 88782 | 90681 | - | espL1 | 100.0 | 97.6 | NP_288154 | (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 88201 | 90387 | + | espL4 | 100.0 | 97.3 | NP_290644 | (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00015 | 12139 | 13193 | - | espR1 | 83.7 | 94.1 | NP_287686 | (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00013 | 102593 | 104013 | + | espX1 | 99.9 | 95.3 | NP_285716 | (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 58405 | 59985 | - | espX4 | 100.0 | 96.5 | NP_290672 | (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 27599 | 28891 | + | espX5 | 100.0 | 97.0 | NP_290699 | (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00013 | 63516 | 64327 | - | espY1 | 99.9 | 87.0 | NP_285753 | (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 78302 | 82550 | - | fdeC | 99.9 | 94.2 | YP_002390132 | (fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88] |
| contig00066 | 900 | 3140 | - | fepA | 100.0 | 96.7 | NP_752600 | (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 104157 | 105113 | + | fepB | 100.0 | 97.5 | NP_752610 | (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 108468 | 109283 | + | fepC | 100.0 | 97.3 | NP_752606 | (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 106466 | 107482 | + | fepD | 100.0 | 96.1 | NP_752608 | (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 107479 | 108471 | + | fepG | 100.0 | 94.1 | NP_752607 | (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 3383 | 4585 | + | fes | 100.0 | 96.7 | NP_752602 | (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00050 | 21169 | 23555 | - | fimD | 90.5 | 98.7 | NP_757244 | (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 20629 | 21162 | - | fimF | 100.0 | 97.9 | NP_757245 | (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 20113 | 20616 | - | fimG | 100.0 | 97.8 | NP_757247 | (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 19191 | 20102 | - | fimH | 100.0 | 97.5 | NP_757248 | (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00035 | 903 | 2753 | + | gspD | 100.0 | 97.0 | YP_404600 | (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 2753 | 4246 | + | gspE | 100.0 | 96.5 | YP_404601 | (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 4246 | 5445 | + | gspF | 100.0 | 96.0 | YP_404602 | (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 5486 | 5941 | + | gspG | 100.0 | 95.0 | YP_404603 | (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 5978 | 6508 | + | gspH | 100.0 | 95.3 | YP_404604 | (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 6505 | 6876 | + | gspI | 100.0 | 95.2 | YP_404605 | (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 6909 | 7478 | + | gspJ | 100.0 | 96.7 | YP_404606 | (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 7475 | 8452 | + | gspK | 100.0 | 96.7 | YP_404607 | (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 8767 | 9627 | + | gspL | 100.0 | 97.1 | YP_404608 | (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 9743 | 10165 | + | gspM | 100.0 | 97.9 | YP_404609 | (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00005 | 69490 | 70530 | - | ompA | 100.0 | 98.1 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00006 | 91657 | 92410 | + | yagV/ecpE | 99.7 | 97.1 | NP_286006 | (yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 90090 | 91733 | + | yagW/ecpD | 100.0 | 99.1 | NP_286007 | (yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 87575 | 90100 | + | yagX/ecpC | 100.0 | 98.8 | NP_286008 | (yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 86881 | 87549 | + | yagY/ecpB | 100.0 | 98.1 | NP_286009 | (yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 86236 | 86823 | + | yagZ/ecpA | 100.0 | 99.0 | NP_286010 | (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 85571 | 86161 | + | ykgK/ecpR | 100.0 | 97.0 | NP_286011 | (ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
## Error in read.table("ID186_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00023 | 35665 | 37093 | + | aslA | 100.0 | 92.9 | AAG10151 | (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00005 | 153477 | 153932 | + | csgB | 99.8 | 83.6 | NP_460114 | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 152072 | 152722 | - | csgD | 100.0 | 81.3 | NP_460113 | (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 151237 | 151653 | - | csgF | 99.0 | 81.2 | NP_460111 | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00005 | 150377 | 151210 | - | csgG | 100.0 | 83.5 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00012 | 99370 | 100116 | - | entA | 100.0 | 95.7 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00099 | 257 | 1003 | + | entA | 100.0 | 98.4 | NP_752614 | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 100116 | 100973 | - | entB | 100.0 | 98.0 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 102607 | 103794 | - | entC | 100.0 | 97.9 | NP_752611 | (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 105 | 875 | - | entD | 100.0 | 95.2 | NP_752599 | (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 100987 | 102597 | - | entE | 100.0 | 95.4 | NP_752612 | (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 4803 | 8656 | + | entF | 99.3 | 95.6 | NP_752604 | (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 105117 | 106367 | - | entS | 100.0 | 95.4 | NP_752609 | (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00003 | 88782 | 90681 | - | espL1 | 100.0 | 97.6 | NP_288154 | (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 88201 | 90387 | + | espL4 | 100.0 | 97.3 | NP_290644 | (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00015 | 12139 | 13193 | - | espR1 | 83.7 | 94.1 | NP_287686 | (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00013 | 102593 | 104013 | + | espX1 | 99.9 | 95.3 | NP_285716 | (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 58405 | 59985 | - | espX4 | 100.0 | 96.5 | NP_290672 | (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00016 | 27599 | 28891 | + | espX5 | 100.0 | 97.0 | NP_290699 | (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00013 | 63516 | 64327 | - | espY1 | 99.9 | 87.0 | NP_285753 | (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 78302 | 82550 | - | fdeC | 99.9 | 94.2 | YP_002390132 | (fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88] |
| contig00066 | 900 | 3140 | - | fepA | 100.0 | 96.7 | NP_752600 | (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 104157 | 105113 | + | fepB | 100.0 | 97.5 | NP_752610 | (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 108468 | 109283 | + | fepC | 100.0 | 97.3 | NP_752606 | (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 106466 | 107482 | + | fepD | 100.0 | 96.1 | NP_752608 | (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00012 | 107479 | 108471 | + | fepG | 100.0 | 94.1 | NP_752607 | (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00066 | 3383 | 4585 | + | fes | 100.0 | 96.7 | NP_752602 | (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073] |
| contig00050 | 21169 | 23555 | - | fimD | 90.5 | 98.7 | NP_757244 | (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 20629 | 21162 | - | fimF | 100.0 | 97.9 | NP_757245 | (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 20113 | 20616 | - | fimG | 100.0 | 97.8 | NP_757247 | (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00050 | 19191 | 20102 | - | fimH | 100.0 | 97.5 | NP_757248 | (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073] |
| contig00035 | 903 | 2753 | + | gspD | 100.0 | 97.0 | YP_404600 | (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 2753 | 4246 | + | gspE | 100.0 | 96.5 | YP_404601 | (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 4246 | 5445 | + | gspF | 100.0 | 96.0 | YP_404602 | (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 5486 | 5941 | + | gspG | 100.0 | 95.0 | YP_404603 | (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 5978 | 6508 | + | gspH | 100.0 | 95.3 | YP_404604 | (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 6505 | 6876 | + | gspI | 100.0 | 95.2 | YP_404605 | (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 6909 | 7478 | + | gspJ | 100.0 | 96.7 | YP_404606 | (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 7475 | 8452 | + | gspK | 100.0 | 96.7 | YP_404607 | (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 8767 | 9627 | + | gspL | 100.0 | 97.1 | YP_404608 | (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00035 | 9743 | 10165 | + | gspM | 100.0 | 97.9 | YP_404609 | (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197] |
| contig00005 | 69490 | 70530 | - | ompA | 100.0 | 98.1 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| contig00006 | 91657 | 92410 | + | yagV/ecpE | 99.7 | 97.1 | NP_286006 | (yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 90090 | 91733 | + | yagW/ecpD | 100.0 | 99.1 | NP_286007 | (yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 87575 | 90100 | + | yagX/ecpC | 100.0 | 98.8 | NP_286008 | (yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 86881 | 87549 | + | yagY/ecpB | 100.0 | 98.1 | NP_286009 | (yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 86236 | 86823 | + | yagZ/ecpA | 100.0 | 99.0 | NP_286010 | (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| contig00006 | 85571 | 86161 | + | ykgK/ecpR | 100.0 | 97.0 | NP_286011 | (ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00033 | 15912 | 16745 | + | csgG | 100.0 | 80.6 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00228 | 594 | 1444 | + | entB | 99.1 | 80.0 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00021 | 40218 | 41263 | + | ompA | 99.0 | 84.5 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
## Error in read.table("ORTHO015E_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00033 | 15912 | 16745 | + | csgG | 100.0 | 80.6 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00228 | 594 | 1444 | + | entB | 99.1 | 80.0 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00021 | 40218 | 41263 | + | ompA | 99.0 | 84.5 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
## Error in read.table("ORTHO037E_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00033 | 15912 | 16745 | + | csgG | 100.0 | 80.6 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00228 | 594 | 1444 | + | entB | 99.1 | 80.0 | NP_752613 | (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] |
| contig00021 | 40218 | 41263 | + | ompA | 99.0 | 84.5 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00107 | 469 | 583 | + | astA | 98.3 | 91.3 | BAA94855 | (astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042] |
| contig00161 | 6225 | 7058 | - | csgG | 100.0 | 80.3 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00048 | 17902 | 18947 | + | ompA | 99.0 | 84.9 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
## Error in read.table("ORTHO05E_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00107 | 469 | 583 | + | astA | 98.3 | 91.3 | BAA94855 | (astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042] |
| contig00161 | 6225 | 7058 | - | csgG | 100.0 | 80.3 | NP_460110 | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
| contig00048 | 17902 | 18947 | + | ompA | 99.0 | 84.9 | AAF37887 | (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] |
| Contig | Start | End | Strand | Gene | Coverage | Identity | Accession | Product |
|---|---|---|---|---|---|---|---|---|
| contig00151 | 8790 | 10222 | + | alg8 | 96.5 | 82.7 | NP_252231 | (alg8) alginate-c5-mannuronan-epimerase AlgG [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1] |
| contig00135 | 3031 | 4437 | - | algA | 97.2 | 81.9 | NP_252241 | (algA) phosphomannose isomerase / guanosine 5’-diphospho-D-mannose pyrophosphorylase [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1] |
| contig00135 | 6486 | 7769 | - | algI | 82.1 | 86.2 | NP_252238 | (algI) alginate o-acetyltransferase AlgI [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1] |
| contig00027 | 5006 | 5587 | + | algU | 100.0 | 82.5 | NP_249453 | (algU) alginate biosynthesis protein AlgZ/FimS [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1] |
| contig00934 | 767 | 1574 | - | fleN | 95.7 | 83.2 | NP_250145 | (fleN) flagellar synthesis regulator FleN [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00061 | 4146 | 5621 | - | fleQ | 99.7 | 80.0 | NP_249788 | (fleQ) transcriptional regulator FleQ [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00198 | 2371 | 2814 | - | flgC | 100.0 | 80.9 | NP_249769 | (flgC) flagellar basal-body rod protein FlgC [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00562 | 975 | 1744 | + | flgG | 97.7 | 86.1 | NP_249773 | (flgG) flagellar basal-body rod protein FlgG [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00562 | 1841 | 2491 | + | flgH | 93.2 | 81.5 | NP_249774 | (flgH) flagellar L-ring protein precursor FlgH [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00562 | 2561 | 3613 | + | flgI | 94.9 | 85.7 | NP_249775 | (flgI) flagellar P-ring protein precursor FlgI [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00381 | 280 | 2396 | - | flhA | 99.3 | 81.6 | NP_250143 | (flhA) flagellar biosynthesis protein FlhA [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00934 | 13 | 723 | - | fliA | 95.0 | 80.3 | NP_250146 | (fliA) flagellar biosynthesis sigma factor FliA [Deoxyhexose linking sugar 209 Da capping structure (AI138)] [Pseudomonas aeruginosa PAO1] |
| contig00844 | 665 | 1682 | + | fliG | 99.8 | 84.7 | NP_249793 | (fliG) flagellar motor switch protein G [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig01095 | 511 | 1479 | - | fliM | 99.6 | 85.9 | NP_250134 | (fliM) flagellar motor switch protein FliM [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig00381 | 4747 | 5464 | - | fliP | 93.1 | 83.1 | NP_250137 | (fliP) flagellar biosynthetic protein FliP [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1] |
| contig02313 | 684 | 885 | + | mbtH-like | 92.2 | 88.6 | NP_251102 | (mbtH-like) MbtH-like protein from the pyoverdine cluster [pyoverdine (IA001)] [Pseudomonas aeruginosa PAO1] |
| contig00682 | 2148 | 2884 | - | motC | 99.3 | 82.0 | NP_250151 | (motC) flagellar motor protein [Deoxyhexose linking sugar 209 Da capping structure (AI138)] [Pseudomonas aeruginosa PAO1] |
| contig00319 | 5118 | 5450 | - | pilH | 91.0 | 80.2 | NP_249100 | (pilH) twitching motility protein PilH [Type IV pili (VF0082)] [Pseudomonas aeruginosa PAO1] |
| contig00661 | 555 | 1873 | + | pvdH | 93.5 | 80.8 | NP_251103 | (pvdH) diaminobutyrate-2-oxoglutarate aminotransferase PvdH [pyoverdine (IA001)] [Pseudomonas aeruginosa PAO1] |
| contig00109 | 469 | 978 | + | pvdS | 90.4 | 82.3 | NP_251116 | (pvdS) extracytoplasmic-function sigma-70 factor [Pyoverdine (VF0094)] [Pseudomonas aeruginosa PAO1] |
| contig00146 | 2638 | 3618 | + | waaF | 94.5 | 81.5 | NP_253699 | (waaF) heptosyltransferase I [LPS (VF0085)] [Pseudomonas aeruginosa PAO1] |
| Symbol | Meaning |
|---|---|
| ~ | novel full length allele similar to match |
| ? | partial match to known allele |
| - | allele missing |
| Scheme | ST | 1 | 2 | 3 | 4 | 5 | 6 | 7 | |
|---|---|---|---|---|---|---|---|---|---|
| ID003II | - | - | |||||||
| ID012II | abaumannii_2 | 1 | Pas_cpn60(1) | Pas_fusA(1) | Pas_gltA(1) | Pas_pyrG(1) | Pas_recA(5) | Pas_rplB(1) | Pas_rpoB(1) |
| ID014II | ecoli | 167 | adk(10) | fumC(11) | gyrB(4) | icd(8) | mdh(8) | purA(13) | recA(2) |
| ID030 | - | - | |||||||
| ID063 | ecoli | 48 | adk(6) | fumC(11) | gyrB(4) | icd(8) | mdh(8) | purA(8) | recA(2) |
| ID089 | abaumannii_2 | - | Pas_cpn60(~199) | Pas_fusA(~186) | Pas_gltA(185) | Pas_pyrG(91) | Pas_recA(~194) | Pas_rplB(101) | Pas_rpoB(169) |
| ID186 | abaumannii_2 | 1 | Pas_cpn60(1) | Pas_fusA(1) | Pas_gltA(1) | Pas_pyrG(1) | Pas_recA(5) | Pas_rplB(1) | Pas_rpoB(1) |
| ID259 | ecloacae | 414 | dnaA(136) | fusA(99) | gyrB(153) | leuS(160) | pyrG(140) | rplB(12) | rpoB(92) |
| ORTHO015E | abaumannii_2 | 52 | Pas_cpn60(3) | Pas_fusA(2) | Pas_gltA(2) | Pas_pyrG(7) | Pas_recA(9) | Pas_rplB(1) | Pas_rpoB(5) |
| ORTHO037E | abaumannii_2 | 1 | Pas_cpn60(1) | Pas_fusA(1) | Pas_gltA(1) | Pas_pyrG(1) | Pas_recA(5) | Pas_rplB(1) | Pas_rpoB(1) |
| ORTHO047E | ecloacae | 515 | dnaA(56) | fusA(38) | gyrB(35) | leuS(58) | pyrG(169) | rplB(12) | rpoB(20) |
| ORTHO05E | - | - | |||||||
| ORTHO082EII | pputida | 12 | argS(8) | gyrB(11) | ileS(52) | nuoC(31) | ppsA(51) | recA(55) | rpoB(20) |
| rpoD(52) |
| Genes | Description | Number |
|---|---|---|
| Core genes | (99% <= strains <= 100%) | 0 |
| Soft core genes | (95% <= strains < 99%) | 0 |
| Shell genes | (15% <= strains < 95%) | 18812 |
| Cloud genes | (0% <= strains < 15%) | 22545 |
| Total genes | (0% <= strains <= 100%) | 41357 |
| Field | Description |
|---|---|
| Region | Numeric code given to insertion sequence (IS) |
| Orientation | The orientation of IS position: Either forward (F) or reverse (F) |
| X-cordinates | The left coordinate of the position |
| Y-coordinates | The right coordinate of the position |
| Gap | The distance between the x and y coordinates |
| CallType | Describes whether a position hit is novel (not in reference) or known (in the reference) |
| LeftGene | Locus tag ID of the gene closest to the left side of the IS position |
| LeftGeneDescription | Description of the gene feature from the left side of the IS position. By default this is the product position |
| RightGene | Locus tag ID of the gene closest to the right side of the IS position |
| RightGeneDescription | Description of the gene feature from the right side of the IS position. By default this is the product position |
| Region | Orientation | X-coordinates | Y-coordinates | Gap | CallType | LeftGene | LeftGeneDescription | RightGene | RightGeneDescription |
|---|---|---|---|---|---|---|---|---|---|
| region_1 | F | 464044 | 464067 | 23 | novel* | IX87_RS02500 | biotin synthase BioB | IX87_RS02500 | biotin synthase BioB |
| region_2 | R | 545223 | 545299 | 76 | novel* | IX87_RS02925 | taurine ABC transporter substrate-binding protein | IX87_RS21895 | IS5-like element ISAba27 family transposase |
| region_3 | F | 1366525 | 1366525 | 0 | novel | IX87_RS07030 | CoA-acylating methylmalonate-semialdehyde dehydrogenase | IX87_RS07035 | aspartate aminotransferase family protein |
| region_4 | R | 1608582 | 1609776 | 1194 | known | IX87_RS08350 | GTP cyclohydrolase I FolE | IX87_RS08365 | ADC family extended-spectrum class C beta-lactamase |
| region_5 | F | 3999793 | 3999801 | -8 | novel | IX87_RS19915 | hypothetical protein | IX87_RS19915 | hypothetical protein |
| Region | Orientation | X-coordinates | Y-coordinates | Gap | CallType | LeftGene | LeftGeneDescription | RightGene | RightGeneDescription |
|---|---|---|---|---|---|---|---|---|---|
| region_1 | F | 836088 | 836097 | -9 | novel | IX87_RS04290 | minor capsid protein | IX87_RS04290 | minor capsid protein |
| region_2 | R | 1608610 | 1609783 | 1173 | known | IX87_RS08350 | GTP cyclohydrolase I FolE | IX87_RS08365 | ADC family extended-spectrum class C beta-lactamase |
| region_3 | F | 1647298 | 1647377 | 79 | novel* | IX87_RS08505 | TetR/AcrR family transcriptional regulator | IX87_RS08505 | TetR/AcrR family transcriptional regulator |
| Region | Orientation | X-coordinates | Y-coordinates | Gap | CallType | LeftGene | LeftGeneDescription | RightGene | RightGeneDescription |
|---|---|---|---|---|---|---|---|---|---|
| region_1 | FALSE | 1524434 | 1524445 | 11 | novel | IX87_RS07860 | EAL domain-containing protein | IX87_RS07860 | EAL domain-containing protein |
| region_1 | FALSE | 1611087 | 1611097 | -10 | novel | IX87_RS08370 | DUF4105 domain-containing protein | IX87_RS08370 | DUF4105 domain-containing protein |
| Region | Orientation | X-coordinates | Y-coordinates | Gap | CallType | LeftGene | LeftGeneDescription | RightGene | RightGeneDescription |
|---|---|---|---|---|---|---|---|---|---|
| region_1 | F | 836082 | 836088 | 6 | novel | IX87_RS04290 | minor capsid protein | IX87_RS04290 | minor capsid protein |
| region_2 | R | 1608602 | 1609765 | 1163 | known | IX87_RS08350 | GTP cyclohydrolase I FolE | IX87_RS08365 | ADC family extended-spectrum class C beta-lactamase |
| region_3 | R | 3393469 | 3394675 | 1206 | known | IX87_RS16895 | EAL domain-containing protein | IX87_RS16910 | TetR/AcrR family transcriptional regulator |
If you have used rMAP, please cite:
Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583
The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite: